From fae8d615e8bb7d8c63fbd7ae07badbeb4c4e3892 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 17 Jan 2025 13:57:13 +0100 Subject: [PATCH 1/6] rearrange --- group_vars/wingedhelix_cluster/vars.yml | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/group_vars/wingedhelix_cluster/vars.yml b/group_vars/wingedhelix_cluster/vars.yml index 16a0909..f3a22bd 100644 --- a/group_vars/wingedhelix_cluster/vars.yml +++ b/group_vars/wingedhelix_cluster/vars.yml @@ -246,16 +246,6 @@ group_subfolder_structure: # owner: umcg-pr-dm # subfolders: "{{ analysis_folders['BclDataToPrm']['prm'] }}" # machines: "{{ groups['chaperone'] }}" - # ###################################################################################################################### - # # umcg-lab group - # ###################################################################################################################### - # - group: umcg-lab - # lfs: tmp06 - # user: umcg-lab-ateambot - # type: notification_webhooks - # analysis_phases: [moveSequencingData] - # notification_target: hpc-helpdesk - # machines: "{{ groups['user_interface'] }}" # # Symlinks to enable sending notifications to certain target when notification are enabled for an anlysis phase in NGS_Automated. # @@ -483,7 +473,16 @@ group_notification_targets: # analysis_phases: [copyBclDataToPrm] # notification_target: hpc-helpdesk_and_pr # machines: "{{ groups['chaperone'] }}" - + # ###################################################################################################################### + # # umcg-lab group + # ###################################################################################################################### + # - group: umcg-lab + # lfs: tmp06 + # user: umcg-lab-ateambot + # type: notification_webhooks + # analysis_phases: [moveSequencingData] + # notification_target: hpc-helpdesk + # machines: "{{ groups['user_interface'] }}" # # Cronjobs for functional accounts. # From 06947675993bbbbdd5b6e7ff8f9792c7dea8be31 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 17 Jan 2025 13:58:20 +0100 Subject: [PATCH 2/6] updated bb and cf to new NGS_Automated versioning + updates coming from wingedhelix included, but mostly disabled --- group_vars/betabarrel_cluster/vars.yml | 597 ++++++++++++++---------- group_vars/copperfist_cluster/vars.yml | 606 +++++++++++++++---------- 2 files changed, 742 insertions(+), 461 deletions(-) diff --git a/group_vars/betabarrel_cluster/vars.yml b/group_vars/betabarrel_cluster/vars.yml index c691974..4e8110a 100644 --- a/group_vars/betabarrel_cluster/vars.yml +++ b/group_vars/betabarrel_cluster/vars.yml @@ -18,7 +18,7 @@ lua_version: '5.1.4.9' lmod_version: '8.6.2' easybuild_version: '4.8.0' eb_user: umcg-envsync -extra_easyconfigs_version: 24.03.2 +extra_easyconfigs_version: 24.11.1 extra_easyconfigs_repository: 'take-it-easyconfigs' # extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/" # @@ -53,6 +53,7 @@ group_subfolder_structure: subfolders: "{{ analysis_folders['ConcordanceCheck']['prm'] | union(analysis_folders['NGS_Demultiplexing']['prm']) | union(analysis_folders['NGS_DNA']['prm']) + | union(analysis_folders['NGS_RNA']['prm']) | union(analysis_folders['trendanalysis']['prm']) }}" machines: "{{ groups['chaperone'] }}" ###################################################################################################################### @@ -83,6 +84,7 @@ group_subfolder_structure: subfolders: "{{ analysis_folders['ConcordanceCheck']['prm'] | union(analysis_folders['NGS_Demultiplexing']['prm']) | union(analysis_folders['NGS_DNA']['prm']) + | union(analysis_folders['NGS_RNA']['prm']) | union(analysis_folders['trendanalysis']['prm']) }}" machines: "{{ groups['chaperone'] }}" ###################################################################################################################### @@ -141,6 +143,7 @@ group_subfolder_structure: mode: "{{ MODE_2770_HARD }}" owner: umcg-gst-ateambot subfolders: "{{ analysis_folders['GsRawData']['tmp'] + | union(analysis_folders['NGS_RNA']['tmp']) | union(analysis_folders['GsAnalysisData']['tmp']) }}" machines: "{{ groups['user_interface'] }}" - group: umcg-gst @@ -158,6 +161,7 @@ group_subfolder_structure: mode: "{{ MODE_2770_HARD }}" owner: umcg-genomescan-ateambot subfolders: "{{ analysis_folders['GsRawData']['tmp'] + | union(analysis_folders['NGS_RNA']['tmp']) | union(analysis_folders['GsAnalysisData']['tmp']) }}" machines: "{{ groups['user_interface'] }}" - group: umcg-genomescan @@ -252,7 +256,7 @@ group_notification_targets: lfs: tmp05 user: umcg-atd-ateambot type: notification_webhooks - analysis_phases: [demultiplexing, startPipeline, pipeline, calculateProjectMd5s] + analysis_phases: [demultiplexing, startPipeline, ConcordanceCheck, pipeline, calculateProjectMd5s, startNanoporePipeline] notification_target: hpc-helpdesk machines: "{{ groups['user_interface'] }}" - group: umcg-atd @@ -266,7 +270,7 @@ group_notification_targets: lfs: prm05 user: umcg-atd-dm type: notification_webhooks - analysis_phases: [copyRawDataToPrm, copyRawDataToTmp, copyProjectDataToPrm] + analysis_phases: [copyRawDataToPrm, copyRawDataToTmp, copyProjectDataToPrm, copyRawNanoporeDataToPrm, copyRawNanoporeDataToTmp, checkRawdata] notification_target: hpc-helpdesk machines: "{{ groups['chaperone'] }}" ###################################################################################################################### @@ -276,7 +280,7 @@ group_notification_targets: lfs: tmp05 user: umcg-gd-ateambot type: notification_webhooks - analysis_phases: [startPipeline, calculateProjectMd5s] + analysis_phases: [startPipeline, ConcordanceCheck, calculateProjectMd5s, startNanoporePipeline] notification_target: hpc-helpdesk machines: "{{ groups['user_interface'] }}" - group: umcg-gd @@ -297,7 +301,7 @@ group_notification_targets: lfs: prm05 user: umcg-gd-dm type: notification_webhooks - analysis_phases: [copyRawDataToTmp] + analysis_phases: [copyRawDataToTmp, copyRawNanoporeDataToPrm, copyRawNanoporeDataToTmp, checkRawdata] notification_target: hpc-helpdesk machines: "{{ groups['chaperone'] }}" - group: umcg-gd @@ -400,7 +404,7 @@ group_notification_targets: lfs: tmp05 user: umcg-genomescan-ateambot type: notification_webhooks - analysis_phases: [PullAndProcessGsRawData, PullAndProcessGsAnalysisData, startDragenPipeline, startNextflowDragenPipeline, pipeline, calculateProjectMd5s] + analysis_phases: [PullAndProcessGsRawData, PullAndProcessGsAnalysisData, startDragenPipeline, startPipeline, startNextflowDragenPipeline, pipeline, calculateProjectMd5s] notification_target: hpc-helpdesk_and_gd-ngs-dataverwerking machines: "{{ groups['user_interface'] }}" - group: umcg-genomescan @@ -454,23 +458,23 @@ group_notification_targets: ###################################################################################################################### # umcg-pr group ###################################################################################################################### - - group: umcg-pr - lfs: dat55 - user: umcg-pr-dm - type: notification_webhooks - analysis_phases: [moveAndCheckSamplesheets] - notification_target: hpc-helpdesk_and_pr - machines: "{{ groups['chaperone'] }}" - - group: umcg-pr - lfs: prm55 - user: umcg-pr-dm - type: notification_webhooks - analysis_phases: [copyBclDataToPrm] - notification_target: hpc-helpdesk_and_pr - machines: "{{ groups['chaperone'] }}" - ###################################################################################################################### - # umcg-lab group - ###################################################################################################################### + # - group: umcg-pr + # lfs: dat55 + # user: umcg-pr-dm + # type: notification_webhooks + # analysis_phases: [moveAndCheckSamplesheets] + # notification_target: hpc-helpdesk_and_pr + # machines: "{{ groups['chaperone'] }}" + # - group: umcg-pr + # lfs: prm55 + # user: umcg-pr-dm + # type: notification_webhooks + # analysis_phases: [copyBclDataToPrm] + # notification_target: hpc-helpdesk_and_pr + # machines: "{{ groups['chaperone'] }}" + # ###################################################################################################################### + # # umcg-lab group + # ###################################################################################################################### - group: umcg-lab lfs: tmp05 user: umcg-lab-ateambot @@ -483,135 +487,135 @@ group_notification_targets: # group_module_versions: umcg-gd: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 NGS_DNA: 4.2.2 ConcordanceCheck: 2.2.1 ngs-utils: 24.02.2 NGS_Demultiplexing: 2.5.4 umcg-gap: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 GAP: 2.7.0 AGCT: 1.3.0 ngs-utils: 24.02.2 umcg-genomescan: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 nf_ngs_dna: 1.0.0 + # NGS_RNA: 4.1.2 NGS_DNA: 4.2.2 - ngs-utils: 24.02.2 + ngs-utils: 24.03.1 umcg-atd: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.3.1 # Default NGS_Automated version. + NGS_DNA: beta # Overruling NGS_Automated version for NGS_Automated-NGS_DNA bundles. NGS_DNA: 4.2.2 - ConcordanceCheck: 2.2.1 + ConcordanceCheck: 3.0.0 ngs-utils: 24.02.2 NGS_Demultiplexing: 2.5.4 umcg-gsad: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.3.1 GAP: 2.7.0 AGCT: 1.3.0 ngs-utils: 24.02.2 umcg-gst: - NGS_Automated: 4.2.0 - nf_ngs_dna: 1.0.0 + NGS_Automated: + default: 4.3.1 + nf_ngs_dna: 1.1.0 NGS_DNA: 4.2.2 + # NGS_RNA: 4.1.2 ngs-utils: 24.02.2 umcg-labgnkbh: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 ngs-utils: 24.02.2 NGS_Demultiplexing: 2.5.4 umcg-patho: - NGS_Automated: 4.2.0 - ngs-utils: 24.02.2 + NGS_Automated: + default: 4.2.0 + ngs-utils: 24.03.1 # umcg-pr: - # NGS_Automated: 4.1.0 + # NGS_Automated: + # default: 4.1.0 # ngs-utils: 24.02.2 umcg-lab: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.3.0 crontabs: ###################################################################################################################### # umcg-atd group ###################################################################################################################### - - name: benikdown # Unique ID required to update existing cronjob: do not modify. + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/benikdown.sh" + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-atd -c" + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-atd -c" - name: NGS_Automated_moveAndCheckSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-atd" - name: NGS_Automated_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-NGS_Demultiplexing-{{ group_module_versions['umcg-atd']['NGS_Demultiplexing'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_Demultiplexing'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_Demultiplexing-{{ group_module_versions['umcg-atd']['NGS_Demultiplexing'] }}; demultiplexing.sh -g umcg-atd" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: '*/5' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-atd -c" - - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: 0 - hour: 6 - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/FileSystemCheckGD.sh" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-atd -p NGS_Demultiplexing" + - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; startPipeline.sh -g umcg-atd -p NGS_DNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-atd -p NGS_DNA" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-atd -c" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; - copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -a -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp05 -f run01.processGsRawData.finished -p DRAGEN; copySamplesheetsForBatchToPrm.sh -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp05" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. @@ -619,15 +623,36 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-bare; copyProjectDataToPrm.sh -g umcg-atd -p NGS_DNA" - - name: NGS_Automated_copyProjectDataToPrm_external # Unique ID required to update existing cronjob: do not modify. + - name: NGS_Automated_copyProjectDataToPrm_external_DNA # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-bare; copyProjectDataToPrm.sh -g umcg-atd -p NGS_DNA -r /groups/umcg-gst/tmp05" + # - name: NGS_Automated_copyProjectDataToPrm_external_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_RNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-bare; + # copyProjectDataToPrm.sh -g umcg-atd -p NGS_RNA -r /groups/umcg-gst/tmp05" + - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: 0 + hour: 6 + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/FileSystemCheckGD.sh" + - name: benikdown # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: '*/5' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/benikdown.sh" + ##### Trendanalysis ##### - name: NGS_Automated_copyQCDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" @@ -635,7 +660,7 @@ crontabs: minute: '0' hour: '6' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyQCDataToTmp.sh -g umcg-atd" - name: NGS_Automated_trendAnalyse # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot @@ -644,7 +669,7 @@ crontabs: minute: '0' hour: '12' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; trendAnalyse.sh -g umcg-atd" - name: NGS_Automated_copyTrendAnalysisDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm @@ -653,7 +678,7 @@ crontabs: minute: '0' hour: '18' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyTrendAnalysisDataToPrm.sh -g umcg-atd" - name: NGS_DNA_GavinSA # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot @@ -676,12 +701,13 @@ crontabs: # ToDo: improve job with "module load" and remove "sh" job: /bin/bash -c "{{ configure_env_in_cronjob }}; cleanupSamplesheets.sh -g umcg-atd" + ##### ConcordanceCheck ##### - name: ConcordanceCheck_ParseDarwinSamplesheet # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}-bare; ParseDarwinSamplesheet.sh -g umcg-atd -a umcg-gsad" - name: ConcordanceCheck_ConcordanceCheck # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot @@ -695,15 +721,8 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}-bare; copyConcordanceCheckData.sh -g umcg-atd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-ateambot - machines: "{{ groups['user_interface'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-atd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" @@ -711,13 +730,6 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-atd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-atd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" @@ -725,91 +737,128 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-atd" + ##### Nanopore ##### + # - name: NGS_Automated_copyRawNanoporeDataToPrm_10 # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-atd -r 10.73.57.10" + # - name: NGS_Automated_copyRawNanoporeDataToPrm_11 # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-atd -r 10.73.57.11" + # - name: NGS_Automated_copyRawNanoporeDataToTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToTmp.sh -g umcg-atd" + # - name: NGS_Automated_startNanoporePipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # startNanoporePipeline.sh -g umcg-atd" + # - name: NGS_Automated_cleanupNanoporeDataOnTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # # ToDo: improve job with "module load" and remove "sh" + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # cleanupDataOnTmp.sh -g umcg-atd -p nanopore" + # - name: NGS_Automated_nanoporeCalculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-atd -p nanopore" + # - name: NGS_Automated_nanoporeCopyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-atd -p nanopore" ###################################################################################################################### # umcg-gd group ###################################################################################################################### - - name: benikdown # Unique ID required to update existing cronjob: do not modify. + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-gd -c" + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/benikdown.sh" + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-gd -c" - name: NGS_Automated_moveAndCheckSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gd" - name: NGS_Automated_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-NGS_Demultiplexing-{{ group_module_versions['umcg-gd']['NGS_Demultiplexing'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['NGS_Demultiplexing'] | default(group_module_versions['umcg-gd']['NGS_Automated']['default']) }}-NGS_Demultiplexing-{{ group_module_versions['umcg-gd']['NGS_Demultiplexing'] }}; demultiplexing.sh -g umcg-gd" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: '*/5' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-gd -c" - - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: 0 - hour: 6 - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/FileSystemCheckGD.sh" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-gd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-gd -p NGS_Demultiplexing" + - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-gd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; startPipeline.sh -g umcg-gd -p NGS_DNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gd -p NGS_DNA" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-gd -c" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-gd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -a -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-genomescan/tmp05 -f run01.processGsRawData.finished -p DRAGEN; copySamplesheetsForBatchToPrm.sh -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-genomescan/tmp05" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. @@ -817,44 +866,84 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gd -p NGS_DNA" + # - name: NGS_Automated_copyProjectDataToPrm_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-gd -p NGS_RNA" - name: NGS_Automated_copyProjectDataToPrm_external # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gd -p NGS_DNA -r /groups/umcg-genomescan/tmp05" + # - name: NGS_Automated_copyProjectDataToPrm_RNA_external # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-gd -p NGS_RNA -r /groups/umcg-genomescan/tmp05" + - name: benikdown # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: '*/5' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/benikdown.sh" + - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: 0 + hour: 6 + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/FileSystemCheckGD.sh" + - name: NGS_Automated_cleanupDataOnTmp # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-ateambot + machines: "{{ groups['user_interface'] | default([]) }}" + minute: '*/10' + # ToDo: improve job with "module load" and remove "sh" + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + cleanupDataOnTmp.sh -g umcg-gd -p NGS_DNA" + - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + # ToDo: improve job with "module load" and remove "sh" + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + cleanupSamplesheets.sh -g umcg-gd" + ##### Trendanalysis ##### - name: NGS_Automated_copyQCDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" - disabled: true # cronjob should be active on only one chaperone machine. Currently this is cf-chaperone weekday: '0' minute: '0' hour: '6' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyQCDataToTmp.sh -g umcg-gd" - name: NGS_Automated_trendAnalyse # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" - disabled: true # cronjob should be active on only one chaperone machine. Currently this is cf-chaperone weekday: '0' minute: '0' hour: '12' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; trendAnalyse.sh -g umcg-gd" - name: NGS_Automated_copyTrendAnalysisDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" - disabled: true # cronjob should be active on only one chaperone machine. Currently this is cf-chaperone weekday: '0' minute: '0' hour: '18' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyTrendAnalysisDataToPrm.sh -g umcg-gd" - name: NGS_DNA_GavinSA # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot @@ -863,27 +952,13 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_DNA/{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; GavinSA.sh -g umcg-gd -t tmp05" - - name: NGS_Automated_cleanupDataOnTmp # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['user_interface'] | default([]) }}" - minute: '*/10' - # ToDo: improve job with "module load" and remove "sh" - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - cleanupDataOnTmp.sh -g umcg-gd -p NGS_DNA" - - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - # ToDo: improve job with "module load" and remove "sh" - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - cleanupSamplesheets.sh -g umcg-gd" + ##### ConcordanceCheck ##### - name: ConcordanceCheck_ParseDarwinSamplesheet # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}-bare; ParseDarwinSamplesheet.sh -g umcg-gd -a umcg-gap" - name: ConcordanceCheck_ConcordanceCheck # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot @@ -897,15 +972,8 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}-bare; copyConcordanceCheckData.sh -g umcg-gd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['user_interface'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-gd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" @@ -913,13 +981,6 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-gd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-gd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" @@ -927,6 +988,49 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-gd" + ##### Nanopore ##### + # - name: NGS_Automated_copyRawNanoporeDataToPrm # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 145.39.79.24" + # - name: NGS_Automated_copyRawNanoporeDataToTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToTmp.sh -g umcg-gd" + # - name: NGS_Automated_startNanoporePipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # startNanoporePipeline.sh -g umcg-gd" + # - name: NGS_Automated_cleanupNanoporeDataOnTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # # ToDo: improve job with "module load" and remove "sh" + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # cleanupDataOnTmp.sh -g umcg-gd -p nanopore" + # - name: NGS_Automated_nanoporeCalculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-gd -p nanopore" + # - name: NGS_Automated_nanoporeCopyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-gd -p nanopore" ###################################################################################################################### # umcg-gsad group ###################################################################################################################### @@ -935,70 +1039,70 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gsad" - name: AGCT_arrayConversion # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-AGCT-{{ group_module_versions['umcg-gsad']['AGCT'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['AGCT'] | default(group_module_versions['umcg-gsad']['NGS_Automated']['default']) }}-AGCT-{{ group_module_versions['umcg-gsad']['AGCT'] }}; arrayConversion.sh -g umcg-gsad" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gsad']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-gsad -p AGCT" - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; copyRawDataToTmp.sh -g umcg-gsad -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-gsad -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gsad']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; startPipeline.sh -g umcg-gsad -p GAP" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gsad -p GAP" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gsad -p GAP" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gsad -c" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gsad -c" - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm @@ -1015,70 +1119,70 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gap" - name: AGCT_arrayConversion # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-AGCT-{{ group_module_versions['umcg-gap']['AGCT'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['AGCT'] | default(group_module_versions['umcg-gap']['NGS_Automated']['default']) }}-AGCT-{{ group_module_versions['umcg-gap']['AGCT'] }}; arrayConversion.sh -g umcg-gap" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gap']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-gap -p AGCT" - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; copyRawDataToTmp.sh -g umcg-gap -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-gap -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gap']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; startPipeline.sh -g umcg-gap -p GAP" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gap -p GAP" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gap -p GAP" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gap -c" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gap -c" - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm @@ -1095,50 +1199,64 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gst" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gst -c" - name: NGS_Automated_PullAndProcessGsRawData # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; PullAndProcessGsRawData.sh -g umcg-gst" - name: NGS_Automated_PullAndProcessGsAnalysisData # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; PullAndProcessGsAnalysisData.sh -g umcg-gst" - name: NGS_Automated_startDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gst']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-gst']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-gst']['NGS_DNA'] }}; startDragenPipeline.sh -g umcg-gst" - name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-gst']['nf_ngs_dna'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['nf_ngs_dna'] | default(group_module_versions['umcg-gst']['NGS_Automated']['default']) }}-nf_ngs_dna-{{ group_module_versions['umcg-gst']['nf_ngs_dna'] }}; startNextflowDragenPipeline.sh -g umcg-gst" + # - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gst-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['NGS_RNA'] | default(group_module_versions['umcg-gst']['NGS_Automated']['default']) }}-NGS_RNA-{{ group_module_versions['umcg-gst']['NGS_RNA'] }}; + # startPipeline.sh -g umcg-gst -p NGS_RNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gst -p NGS_DNA" + # - name: NGS_Automated_calculateProjectMd5s_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gst-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-gst -p NGS_RNA" ###################################################################################################################### # umcg-genomescan group ###################################################################################################################### @@ -1147,57 +1265,78 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-genomescan" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-genomescan -c" - name: NGS_Automated_PullAndProcessGsRawData # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; PullAndProcessGsRawData.sh -g umcg-genomescan" - name: NGS_Automated_PullAndProcessGsAnalysisData # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; PullAndProcessGsAnalysisData.sh -g umcg-genomescan" - name: NGS_Automated_startDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-genomescan']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-genomescan']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-genomescan']['NGS_DNA'] }}; startDragenPipeline.sh -g umcg-genomescan" - name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-genomescan']['nf_ngs_dna'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['nf_ngs_dna'] | default(group_module_versions['umcg-genomescan']['NGS_Automated']['default']) }}-nf_ngs_dna-{{ group_module_versions['umcg-genomescan']['nf_ngs_dna'] }}; startNextflowDragenPipeline.sh -g umcg-genomescan" + # - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-genomescan-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['NGS_RNA'] | default(group_module_versions['umcg-genomescan']['NGS_Automated']['default']) }}-NGS_RNA-{{ group_module_versions['umcg-genomescan']['NGS_RNA'] }}; + # startPipeline.sh -g umcg-genomescan -p NGS_RNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-genomescan -p NGS_DNA" + # - name: NGS_Automated_calculateProjectMd5s_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-genomescan-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-genomescan -p NGS_RNA" - name: NGS_Automated_cleanupDataOnTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; cleanupDataOnTmp.sh -g umcg-genomescan -p NGS_DNA" + # - name: NGS_Automated_cleanupDataOnTmp_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-genomescan-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; + # cleanupDataOnTmp.sh -g umcg-genomescan -p NGS_RNA" ##################################################################################################################### # umcg-labgnkbh group ##################################################################################################################### @@ -1206,29 +1345,29 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat45" + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; + moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat47" - name: NGS_Demultiplexing_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-NGS_Demultiplexing-{{ group_module_versions['umcg-labgnkbh']['NGS_Demultiplexing'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['NGS_Demultiplexing'] | default(group_module_versions['umcg-labgnkbh']['NGS_Automated']['default']) }}-NGS_Demultiplexing-{{ group_module_versions['umcg-labgnkbh']['NGS_Demultiplexing'] }}; demultiplexing.sh -g umcg-labgnkbh" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-labgnkbh -c -d dat45 -p prm45" + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-labgnkbh -c -d dat47 -p prm47" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare; - copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm45 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; + copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm47 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" ###################################################################################################################### # umcg-patho group ###################################################################################################################### @@ -1237,22 +1376,22 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-patho -d dat35" + module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; + moveAndCheckSamplesheets.sh -g umcg-patho -d dat37" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-patho -c -d dat35 -p prm35" + module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-patho -c -d dat37 -p prm37" - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare; - copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm35" + module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; + copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm37" ###################################################################################################################### # umcg-pr group ###################################################################################################################### @@ -1261,22 +1400,22 @@ crontabs: # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/5' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; - # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare; - # moveAndCheckSamplesheets.sh -g umcg-pr -d dat55" + # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; + # moveAndCheckSamplesheets.sh -g umcg-pr -d dat57" # - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; - # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare; - # notifications.sh -g umcg-pr -c -d dat55 -p prm55" + # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; + # notifications.sh -g umcg-pr -c -d dat57 -p prm57" # - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; - # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare; - # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm55" + # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; + # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm57" ###################################################################################################################### # umcg-lab group ###################################################################################################################### @@ -1285,7 +1424,7 @@ crontabs: machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-lab']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-lab']['NGS_Automated']['default'] }}-bare; moveSequencingData.sh -t tmp05" # diff --git a/group_vars/copperfist_cluster/vars.yml b/group_vars/copperfist_cluster/vars.yml index 64c83ce..1a6a78f 100644 --- a/group_vars/copperfist_cluster/vars.yml +++ b/group_vars/copperfist_cluster/vars.yml @@ -18,7 +18,7 @@ lua_version: '5.1.4.9' lmod_version: '8.6.2' easybuild_version: '4.8.0' eb_user: umcg-envsync -extra_easyconfigs_version: 24.03.2 +extra_easyconfigs_version: 24.11.1 extra_easyconfigs_repository: 'take-it-easyconfigs' # extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/" # @@ -53,6 +53,7 @@ group_subfolder_structure: subfolders: "{{ analysis_folders['ConcordanceCheck']['prm'] | union(analysis_folders['NGS_Demultiplexing']['prm']) | union(analysis_folders['NGS_DNA']['prm']) + | union(analysis_folders['NGS_RNA']['prm']) | union(analysis_folders['trendanalysis']['prm']) }}" machines: "{{ groups['chaperone'] }}" ###################################################################################################################### @@ -83,6 +84,7 @@ group_subfolder_structure: subfolders: "{{ analysis_folders['ConcordanceCheck']['prm'] | union(analysis_folders['NGS_Demultiplexing']['prm']) | union(analysis_folders['NGS_DNA']['prm']) + | union(analysis_folders['NGS_RNA']['prm']) | union(analysis_folders['trendanalysis']['prm']) }}" machines: "{{ groups['chaperone'] }}" ###################################################################################################################### @@ -141,6 +143,7 @@ group_subfolder_structure: mode: "{{ MODE_2770_HARD }}" owner: umcg-gst-ateambot subfolders: "{{ analysis_folders['GsRawData']['tmp'] + | union(analysis_folders['NGS_RNA']['tmp']) | union(analysis_folders['GsAnalysisData']['tmp']) }}" machines: "{{ groups['user_interface'] }}" - group: umcg-gst @@ -158,6 +161,7 @@ group_subfolder_structure: mode: "{{ MODE_2770_HARD }}" owner: umcg-genomescan-ateambot subfolders: "{{ analysis_folders['GsRawData']['tmp'] + | union(analysis_folders['NGS_RNA']['tmp']) | union(analysis_folders['GsAnalysisData']['tmp']) }}" machines: "{{ groups['user_interface'] }}" - group: umcg-genomescan @@ -252,7 +256,7 @@ group_notification_targets: lfs: tmp06 user: umcg-atd-ateambot type: notification_webhooks - analysis_phases: [demultiplexing, startPipeline, pipeline, calculateProjectMd5s] + analysis_phases: [demultiplexing, startPipeline, ConcordanceCheck, pipeline, calculateProjectMd5s, startNanoporePipeline] notification_target: hpc-helpdesk machines: "{{ groups['user_interface'] }}" - group: umcg-atd @@ -266,7 +270,7 @@ group_notification_targets: lfs: prm06 user: umcg-atd-dm type: notification_webhooks - analysis_phases: [copyRawDataToPrm, copyRawDataToTmp, copyProjectDataToPrm] + analysis_phases: [copyRawDataToPrm, copyRawDataToTmp, copyProjectDataToPrm, copyRawNanoporeDataToPrm, copyRawNanoporeDataToTmp, checkRawdata] notification_target: hpc-helpdesk machines: "{{ groups['chaperone'] }}" ###################################################################################################################### @@ -276,7 +280,7 @@ group_notification_targets: lfs: tmp06 user: umcg-gd-ateambot type: notification_webhooks - analysis_phases: [startPipeline, calculateProjectMd5s] + analysis_phases: [startPipeline, ConcordanceCheck, calculateProjectMd5s, startNanoporePipeline] notification_target: hpc-helpdesk machines: "{{ groups['user_interface'] }}" - group: umcg-gd @@ -297,7 +301,7 @@ group_notification_targets: lfs: prm06 user: umcg-gd-dm type: notification_webhooks - analysis_phases: [copyRawDataToTmp] + analysis_phases: [copyRawDataToTmp, copyRawNanoporeDataToPrm, copyRawNanoporeDataToTmp, checkRawdata] notification_target: hpc-helpdesk machines: "{{ groups['chaperone'] }}" - group: umcg-gd @@ -400,7 +404,7 @@ group_notification_targets: lfs: tmp06 user: umcg-genomescan-ateambot type: notification_webhooks - analysis_phases: [PullAndProcessGsRawData, PullAndProcessGsAnalysisData, startDragenPipeline, startNextflowDragenPipeline, pipeline, calculateProjectMd5s] + analysis_phases: [PullAndProcessGsRawData, PullAndProcessGsAnalysisData, startDragenPipeline, startPipeline, startNextflowDragenPipeline, pipeline, calculateProjectMd5s] notification_target: hpc-helpdesk_and_gd-ngs-dataverwerking machines: "{{ groups['user_interface'] }}" - group: umcg-genomescan @@ -454,23 +458,23 @@ group_notification_targets: ###################################################################################################################### # umcg-pr group ###################################################################################################################### - - group: umcg-pr - lfs: dat56 - user: umcg-pr-dm - type: notification_webhooks - analysis_phases: [moveAndCheckSamplesheets] - notification_target: hpc-helpdesk_and_pr - machines: "{{ groups['chaperone'] }}" - - group: umcg-pr - lfs: prm56 - user: umcg-pr-dm - type: notification_webhooks - analysis_phases: [copyBclDataToPrm] - notification_target: hpc-helpdesk_and_pr - machines: "{{ groups['chaperone'] }}" - ###################################################################################################################### - # umcg-lab group - ###################################################################################################################### + # - group: umcg-pr + # lfs: dat56 + # user: umcg-pr-dm + # type: notification_webhooks + # analysis_phases: [moveAndCheckSamplesheets] + # notification_target: hpc-helpdesk_and_pr + # machines: "{{ groups['chaperone'] }}" + # - group: umcg-pr + # lfs: prm56 + # user: umcg-pr-dm + # type: notification_webhooks + # analysis_phases: [copyBclDataToPrm] + # notification_target: hpc-helpdesk_and_pr + # machines: "{{ groups['chaperone'] }}" + # ###################################################################################################################### + # # umcg-lab group + # ###################################################################################################################### - group: umcg-lab lfs: tmp06 user: umcg-lab-ateambot @@ -483,135 +487,135 @@ group_notification_targets: # group_module_versions: umcg-gd: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 NGS_DNA: 4.2.2 ConcordanceCheck: 2.2.1 ngs-utils: 24.02.2 NGS_Demultiplexing: 2.5.4 umcg-gap: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 GAP: 2.7.0 AGCT: 1.3.0 ngs-utils: 24.02.2 umcg-genomescan: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 nf_ngs_dna: 1.0.0 + # NGS_RNA: 4.1.2 NGS_DNA: 4.2.2 - ngs-utils: 24.02.2 + ngs-utils: 24.03.1 umcg-atd: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.3.1 # Default NGS_Automated version. + NGS_DNA: beta # Overruling NGS_Automated version for NGS_Automated-NGS_DNA bundles. NGS_DNA: 4.2.2 - ConcordanceCheck: 2.2.1 + ConcordanceCheck: 3.0.0 ngs-utils: 24.02.2 NGS_Demultiplexing: 2.5.4 umcg-gsad: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.3.1 GAP: 2.7.0 AGCT: 1.3.0 ngs-utils: 24.02.2 umcg-gst: - NGS_Automated: 4.2.0 - nf_ngs_dna: 1.0.0 + NGS_Automated: + default: 4.3.1 + nf_ngs_dna: 1.1.0 NGS_DNA: 4.2.2 + # NGS_RNA: 4.1.2 ngs-utils: 24.02.2 umcg-labgnkbh: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.2.0 ngs-utils: 24.02.2 NGS_Demultiplexing: 2.5.4 umcg-patho: - NGS_Automated: 4.2.0 - ngs-utils: 24.02.2 + NGS_Automated: + default: 4.2.0 + ngs-utils: 24.03.1 # umcg-pr: - # NGS_Automated: 4.1.0 + # NGS_Automated: + # default: 4.1.0 # ngs-utils: 24.02.2 umcg-lab: - NGS_Automated: 4.2.0 + NGS_Automated: + default: 4.3.0 crontabs: ###################################################################################################################### # umcg-atd group ###################################################################################################################### - - name: benikdown # Unique ID required to update existing cronjob: do not modify. + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/benikdown.sh" + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-atd -c" + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-atd -c" - name: NGS_Automated_moveAndCheckSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-atd" - name: NGS_Automated_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-NGS_Demultiplexing-{{ group_module_versions['umcg-atd']['NGS_Demultiplexing'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_Demultiplexing'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_Demultiplexing-{{ group_module_versions['umcg-atd']['NGS_Demultiplexing'] }}; demultiplexing.sh -g umcg-atd" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: '*/5' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-atd -c" - - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: 0 - hour: 6 - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/FileSystemCheckGD.sh" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-atd -p NGS_Demultiplexing" + - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; startPipeline.sh -g umcg-atd -p NGS_DNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-atd -p NGS_DNA" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-atd -c" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; - copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -a -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06 -f run01.processGsRawData.finished -p DRAGEN; copySamplesheetsForBatchToPrm.sh -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. @@ -619,15 +623,36 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-bare; copyProjectDataToPrm.sh -g umcg-atd -p NGS_DNA" - - name: NGS_Automated_copyProjectDataToPrm_external # Unique ID required to update existing cronjob: do not modify. + - name: NGS_Automated_copyProjectDataToPrm_external_DNA # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-bare; copyProjectDataToPrm.sh -g umcg-atd -p NGS_DNA -r /groups/umcg-gst/tmp06" + # - name: NGS_Automated_copyProjectDataToPrm_external_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_RNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-bare; + # copyProjectDataToPrm.sh -g umcg-atd -p NGS_RNA -r /groups/umcg-gst/tmp06" + - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: 0 + hour: 6 + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/FileSystemCheckGD.sh" + - name: benikdown # Unique ID required to update existing cronjob: do not modify. + user: umcg-atd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: '*/5' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/benikdown.sh" + ##### Trendanalysis ##### - name: NGS_Automated_copyQCDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" @@ -635,7 +660,7 @@ crontabs: minute: '0' hour: '6' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyQCDataToTmp.sh -g umcg-atd" - name: NGS_Automated_trendAnalyse # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot @@ -644,7 +669,7 @@ crontabs: minute: '0' hour: '12' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; trendAnalyse.sh -g umcg-atd" - name: NGS_Automated_copyTrendAnalysisDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm @@ -653,7 +678,7 @@ crontabs: minute: '0' hour: '18' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; copyTrendAnalysisDataToPrm.sh -g umcg-atd" - name: NGS_DNA_GavinSA # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot @@ -676,12 +701,13 @@ crontabs: # ToDo: improve job with "module load" and remove "sh" job: /bin/bash -c "{{ configure_env_in_cronjob }}; cleanupSamplesheets.sh -g umcg-atd" + ##### ConcordanceCheck ##### - name: ConcordanceCheck_ParseDarwinSamplesheet # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}-bare; ParseDarwinSamplesheet.sh -g umcg-atd -a umcg-gsad" - name: ConcordanceCheck_ConcordanceCheck # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot @@ -695,15 +721,8 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}-bare; copyConcordanceCheckData.sh -g umcg-atd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-ateambot - machines: "{{ groups['user_interface'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-atd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" @@ -711,13 +730,6 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-atd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-atd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-atd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm machines: "{{ groups['chaperone'] | default([]) }}" @@ -725,91 +737,128 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-atd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-atd" + ##### Nanopore ##### + # - name: NGS_Automated_copyRawNanoporeDataToPrm_10 # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-atd -r 10.73.57.10" + # - name: NGS_Automated_copyRawNanoporeDataToPrm_11 # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-atd -r 10.73.57.11" + # - name: NGS_Automated_copyRawNanoporeDataToTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToTmp.sh -g umcg-atd" + # - name: NGS_Automated_startNanoporePipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # startNanoporePipeline.sh -g umcg-atd" + # - name: NGS_Automated_cleanupNanoporeDataOnTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # # ToDo: improve job with "module load" and remove "sh" + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # cleanupDataOnTmp.sh -g umcg-atd -p nanopore" + # - name: NGS_Automated_nanoporeCalculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-atd -p nanopore" + # - name: NGS_Automated_nanoporeCopyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. + # user: umcg-atd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-atd -p nanopore" ###################################################################################################################### # umcg-gd group ###################################################################################################################### - - name: benikdown # Unique ID required to update existing cronjob: do not modify. + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-gd -c" + - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/benikdown.sh" + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-gd -c" - name: NGS_Automated_moveAndCheckSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gd" - name: NGS_Automated_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-NGS_Demultiplexing-{{ group_module_versions['umcg-gd']['NGS_Demultiplexing'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['NGS_Demultiplexing'] | default(group_module_versions['umcg-gd']['NGS_Automated']['default']) }}-NGS_Demultiplexing-{{ group_module_versions['umcg-gd']['NGS_Demultiplexing'] }}; demultiplexing.sh -g umcg-gd" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: '*/5' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-gd -c" - - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" - minute: 0 - hour: 6 - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - ${HOME}/FileSystemCheckGD.sh" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-gd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-gd -p NGS_Demultiplexing" + - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-gd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; startPipeline.sh -g umcg-gd -p NGS_DNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gd -p NGS_DNA" - - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-gd -c" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-gd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -a -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-genomescan/tmp06 -f run01.processGsRawData.finished -p DRAGEN; copySamplesheetsForBatchToPrm.sh -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-genomescan/tmp06" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. @@ -817,15 +866,58 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gd -p NGS_DNA" + # - name: NGS_Automated_copyProjectDataToPrm_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-gd -p NGS_RNA" - name: NGS_Automated_copyProjectDataToPrm_external # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gd -p NGS_DNA -r /groups/umcg-genomescan/tmp06" + # - name: NGS_Automated_copyProjectDataToPrm_RNA_external # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-gd -p NGS_RNA -r /groups/umcg-genomescan/tmp06" + - name: benikdown # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: '*/5' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/benikdown.sh" + - name: FileSystemCheck # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-ateambot + machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" + minute: 0 + hour: 6 + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + ${HOME}/FileSystemCheckGD.sh" + - name: NGS_Automated_cleanupDataOnTmp # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-ateambot + machines: "{{ groups['user_interface'] | default([]) }}" + minute: '*/10' + # ToDo: improve job with "module load" and remove "sh" + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + cleanupDataOnTmp.sh -g umcg-gd -p NGS_DNA" + - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + # ToDo: improve job with "module load" and remove "sh" + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + cleanupSamplesheets.sh -g umcg-gd" + ##### Trendanalysis ##### - name: NGS_Automated_copyQCDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" @@ -833,7 +925,7 @@ crontabs: minute: '0' hour: '6' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyQCDataToTmp.sh -g umcg-gd" - name: NGS_Automated_trendAnalyse # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot @@ -842,7 +934,7 @@ crontabs: minute: '0' hour: '12' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; trendAnalyse.sh -g umcg-gd" - name: NGS_Automated_copyTrendAnalysisDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm @@ -851,7 +943,7 @@ crontabs: minute: '0' hour: '18' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; copyTrendAnalysisDataToPrm.sh -g umcg-gd" - name: NGS_DNA_GavinSA # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot @@ -860,27 +952,13 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_DNA/{{ group_module_versions['umcg-gd']['NGS_DNA'] }}; GavinSA.sh -g umcg-gd -t tmp06" - - name: NGS_Automated_cleanupDataOnTmp # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['user_interface'] | default([]) }}" - minute: '*/10' - # ToDo: improve job with "module load" and remove "sh" - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare; - cleanupDataOnTmp.sh -g umcg-gd -p NGS_DNA" - - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - # ToDo: improve job with "module load" and remove "sh" - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - cleanupSamplesheets.sh -g umcg-gd" + ##### ConcordanceCheck ##### - name: ConcordanceCheck_ParseDarwinSamplesheet # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}-bare; ParseDarwinSamplesheet.sh -g umcg-gd -a umcg-gap" - name: ConcordanceCheck_ConcordanceCheck # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot @@ -894,15 +972,8 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; + module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}-bare; copyConcordanceCheckData.sh -g umcg-gd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-ateambot - machines: "{{ groups['user_interface'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-gd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-ateambot machines: "{{ groups['user_interface'] | default([]) }}" @@ -910,13 +981,6 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-gd" - - name: ConcordanceCheck_notifications # Unique ID required to update existing cronjob: do not modify. - user: umcg-gd-dm - machines: "{{ groups['chaperone'] | default([]) }}" - minute: '*/10' - job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; - notifications.sh -g umcg-gd -c" - name: ConcordanceCheck_cleanup # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" @@ -924,6 +988,49 @@ crontabs: job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-gd" + ##### Nanopore ##### + # - name: NGS_Automated_copyRawNanoporeDataToPrm # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 145.39.79.24" + # - name: NGS_Automated_copyRawNanoporeDataToTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToTmp.sh -g umcg-gd" + # - name: NGS_Automated_startNanoporePipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # startNanoporePipeline.sh -g umcg-gd" + # - name: NGS_Automated_cleanupNanoporeDataOnTmp # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # # ToDo: improve job with "module load" and remove "sh" + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # cleanupDataOnTmp.sh -g umcg-gd -p nanopore" + # - name: NGS_Automated_nanoporeCalculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-gd -p nanopore" + # - name: NGS_Automated_nanoporeCopyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyProjectDataToPrm.sh -g umcg-gd -p nanopore" ###################################################################################################################### # umcg-gsad group ###################################################################################################################### @@ -932,70 +1039,70 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gsad" - name: AGCT_arrayConversion # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-AGCT-{{ group_module_versions['umcg-gsad']['AGCT'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['AGCT'] | default(group_module_versions['umcg-gsad']['NGS_Automated']['default']) }}-AGCT-{{ group_module_versions['umcg-gsad']['AGCT'] }}; arrayConversion.sh -g umcg-gsad" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gsad']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-gsad -p AGCT" - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; copyRawDataToTmp.sh -g umcg-gsad -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-gsad -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gsad']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gsad']['GAP'] }}; startPipeline.sh -g umcg-gsad -p GAP" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gsad -p GAP" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gsad -p GAP" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gsad -c" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gsad -c" - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-gsad-dm @@ -1012,70 +1119,70 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gap" - name: AGCT_arrayConversion # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-AGCT-{{ group_module_versions['umcg-gap']['AGCT'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['AGCT'] | default(group_module_versions['umcg-gap']['NGS_Automated']['default']) }}-AGCT-{{ group_module_versions['umcg-gap']['AGCT'] }}; arrayConversion.sh -g umcg-gap" - name: NGS_Automated_splitAndMoveSamplesheetPerProject # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gap']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-gap -p AGCT" - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; copyRawDataToTmp.sh -g umcg-gap -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" - name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; copyRawDataToPrm.sh -g umcg-gap -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT" - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['GAP'] | default(group_module_versions['umcg-gap']['NGS_Automated']['default']) }}-GAP-{{ group_module_versions['umcg-gap']['GAP'] }}; startPipeline.sh -g umcg-gap -p GAP" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gap -p GAP" - name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; copyProjectDataToPrm.sh -g umcg-gap -p GAP" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gap -c" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gap -c" - name: NGS_Automated_cleanupSamplesheets # Unique ID required to update existing cronjob: do not modify. user: umcg-gap-dm @@ -1092,50 +1199,64 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-gst" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-gst -c" - name: NGS_Automated_PullAndProcessGsRawData # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; PullAndProcessGsRawData.sh -g umcg-gst" - name: NGS_Automated_PullAndProcessGsAnalysisData # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; PullAndProcessGsAnalysisData.sh -g umcg-gst" - name: NGS_Automated_startDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gst']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-gst']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-gst']['NGS_DNA'] }}; startDragenPipeline.sh -g umcg-gst" - name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-gst']['nf_ngs_dna'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['nf_ngs_dna'] | default(group_module_versions['umcg-gst']['NGS_Automated']['default']) }}-nf_ngs_dna-{{ group_module_versions['umcg-gst']['nf_ngs_dna'] }}; startNextflowDragenPipeline.sh -g umcg-gst" + # - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gst-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['NGS_RNA'] | default(group_module_versions['umcg-gst']['NGS_Automated']['default']) }}-NGS_RNA-{{ group_module_versions['umcg-gst']['NGS_RNA'] }}; + # startPipeline.sh -g umcg-gst -p NGS_RNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-gst-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-gst -p NGS_DNA" + # - name: NGS_Automated_calculateProjectMd5s_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gst-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-gst -p NGS_RNA" ###################################################################################################################### # umcg-genomescan group ###################################################################################################################### @@ -1144,57 +1265,78 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; moveAndCheckSamplesheets.sh -g umcg-genomescan" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['chaperone'] | default([]) + groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; notifications.sh -g umcg-genomescan -c" - name: NGS_Automated_PullAndProcessGsRawData # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; PullAndProcessGsRawData.sh -g umcg-genomescan" - name: NGS_Automated_PullAndProcessGsAnalysisData # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; PullAndProcessGsAnalysisData.sh -g umcg-genomescan" - name: NGS_Automated_startDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-genomescan']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-genomescan']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-genomescan']['NGS_DNA'] }}; startDragenPipeline.sh -g umcg-genomescan" - name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-genomescan']['nf_ngs_dna'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['nf_ngs_dna'] | default(group_module_versions['umcg-genomescan']['NGS_Automated']['default']) }}-nf_ngs_dna-{{ group_module_versions['umcg-genomescan']['nf_ngs_dna'] }}; startNextflowDragenPipeline.sh -g umcg-genomescan" + # - name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify. + # user: umcg-genomescan-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['NGS_RNA'] | default(group_module_versions['umcg-genomescan']['NGS_Automated']['default']) }}-NGS_RNA-{{ group_module_versions['umcg-genomescan']['NGS_RNA'] }}; + # startPipeline.sh -g umcg-genomescan -p NGS_RNA" - name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; calculateProjectMd5s.sh -g umcg-genomescan -p NGS_DNA" + # - name: NGS_Automated_calculateProjectMd5s_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-genomescan-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; + # calculateProjectMd5s.sh -g umcg-genomescan -p NGS_RNA" - name: NGS_Automated_cleanupDataOnTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-genomescan-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-bare; + module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; cleanupDataOnTmp.sh -g umcg-genomescan -p NGS_DNA" + # - name: NGS_Automated_cleanupDataOnTmp_RNA # Unique ID required to update existing cronjob: do not modify. + # user: umcg-genomescan-ateambot + # machines: "{{ groups['user_interface'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated']['default'] }}-bare; + # cleanupDataOnTmp.sh -g umcg-genomescan -p NGS_RNA" ##################################################################################################################### # umcg-labgnkbh group ##################################################################################################################### @@ -1203,29 +1345,29 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat46" + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; + moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat47" - name: NGS_Demultiplexing_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-ateambot machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-NGS_Demultiplexing-{{ group_module_versions['umcg-labgnkbh']['NGS_Demultiplexing'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['NGS_Demultiplexing'] | default(group_module_versions['umcg-labgnkbh']['NGS_Automated']['default']) }}-NGS_Demultiplexing-{{ group_module_versions['umcg-labgnkbh']['NGS_Demultiplexing'] }}; demultiplexing.sh -g umcg-labgnkbh" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-labgnkbh -c -d dat46 -p prm46" + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-labgnkbh -c -d dat47 -p prm47" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare; - copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm46 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" + module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; + copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm47 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" ###################################################################################################################### # umcg-patho group ###################################################################################################################### @@ -1234,22 +1376,22 @@ crontabs: machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-patho -d dat36" + module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; + moveAndCheckSamplesheets.sh -g umcg-patho -d dat37" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare; - notifications.sh -g umcg-patho -c -d dat36 -p prm36" + module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; + notifications.sh -g umcg-patho -c -d dat37 -p prm37" - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare; - copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm36" + module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; + copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm37" ###################################################################################################################### # umcg-pr group ###################################################################################################################### @@ -1258,32 +1400,32 @@ crontabs: # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/5' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; - # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare; - # moveAndCheckSamplesheets.sh -g umcg-pr -d dat56" + # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; + # moveAndCheckSamplesheets.sh -g umcg-pr -d dat57" # - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; - # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare; - # notifications.sh -g umcg-pr -c -d dat56 -p prm56" + # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; + # notifications.sh -g umcg-pr -c -d dat57 -p prm57" # - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; - # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare; - # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm56" + # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; + # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm57" ###################################################################################################################### # umcg-lab group ###################################################################################################################### - #- name: NGS_Automated_moveSequencingData # Unique ID required to update existing cronjob: do not modify. - # user: umcg-lab-ateambot - # machines: "{{ groups['user_interface'] | default([]) }}" - # minute: '*/10' - # job: /bin/bash -c "{{ configure_env_in_cronjob }}; - # module load NGS_Automated/{{ group_module_versions['umcg-lab']['NGS_Automated'] }}-bare; - # moveSequencingData.sh -t tmp06" + - name: NGS_Automated_moveSequencingData # Unique ID required to update existing cronjob: do not modify. + user: umcg-lab-ateambot + machines: "{{ groups['user_interface'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-lab']['NGS_Automated']['default'] }}-bare; + moveSequencingData.sh -t tmp06" # # Sources, software and reference data to install/fetch. From 1b7ae451a5cabe493ae5f57b91e0682d3501b42f Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 24 Jan 2025 10:26:07 +0100 Subject: [PATCH 3/6] correcting to the correct storage numbers --- group_vars/betabarrel_cluster/vars.yml | 22 ++++++++++++---------- group_vars/copperfist_cluster/vars.yml | 18 +++++++++--------- group_vars/wingedhelix_cluster/vars.yml | 2 +- 3 files changed, 22 insertions(+), 20 deletions(-) diff --git a/group_vars/betabarrel_cluster/vars.yml b/group_vars/betabarrel_cluster/vars.yml index 4e8110a..2353cca 100644 --- a/group_vars/betabarrel_cluster/vars.yml +++ b/group_vars/betabarrel_cluster/vars.yml @@ -493,6 +493,8 @@ group_module_versions: ConcordanceCheck: 2.2.1 ngs-utils: 24.02.2 NGS_Demultiplexing: 2.5.4 + vip:8.1.0 + umcg-gap: NGS_Automated: default: 4.2.0 @@ -580,7 +582,7 @@ crontabs: machines: "{{ groups['user_interface'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; - module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; + module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated']['NGS_DNA']['vip-umcg-config-gd'] | default(group_module_versions['umcg-atd']['NGS_Automated']['default']) }}-NGS_DNA-{{ group_module_versions['umcg-atd']['NGS_DNA'] }}; splitAndMoveSamplesheetPerProject.sh -g umcg-atd -p NGS_Demultiplexing" - name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-atd-dm @@ -1346,7 +1348,7 @@ crontabs: minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat47" + moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat45" - name: NGS_Demultiplexing_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-ateambot machines: "{{ groups['user_interface'] | default([]) }}" @@ -1360,14 +1362,14 @@ crontabs: minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; - notifications.sh -g umcg-labgnkbh -c -d dat47 -p prm47" + notifications.sh -g umcg-labgnkbh -c -d dat45 -p prm45" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; - copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm47 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" + copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm45 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" ###################################################################################################################### # umcg-patho group ###################################################################################################################### @@ -1377,21 +1379,21 @@ crontabs: minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-patho -d dat37" + moveAndCheckSamplesheets.sh -g umcg-patho -d dat35" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; - notifications.sh -g umcg-patho -c -d dat37 -p prm37" + notifications.sh -g umcg-patho -c -d dat35 -p prm35" - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; - copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm37" + copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm35" ###################################################################################################################### # umcg-pr group ###################################################################################################################### @@ -1401,21 +1403,21 @@ crontabs: # minute: '*/5' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; - # moveAndCheckSamplesheets.sh -g umcg-pr -d dat57" + # moveAndCheckSamplesheets.sh -g umcg-pr -d dat55" # - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; - # notifications.sh -g umcg-pr -c -d dat57 -p prm57" + # notifications.sh -g umcg-pr -c -d dat55 -p prm55" # - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; - # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm57" + # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm55" ###################################################################################################################### # umcg-lab group ###################################################################################################################### diff --git a/group_vars/copperfist_cluster/vars.yml b/group_vars/copperfist_cluster/vars.yml index 1a6a78f..125b1ed 100644 --- a/group_vars/copperfist_cluster/vars.yml +++ b/group_vars/copperfist_cluster/vars.yml @@ -1346,7 +1346,7 @@ crontabs: minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat47" + moveAndCheckSamplesheets.sh -g umcg-labgnkbh -d dat46" - name: NGS_Demultiplexing_demultiplexing # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-ateambot machines: "{{ groups['user_interface'] | default([]) }}" @@ -1360,14 +1360,14 @@ crontabs: minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; - notifications.sh -g umcg-labgnkbh -c -d dat47 -p prm47" + notifications.sh -g umcg-labgnkbh -c -d dat46 -p prm46" - name: NGS_Automated_copyRawDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-labgnkbh-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated']['default'] }}-bare; - copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm47 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" + copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm46 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}" ###################################################################################################################### # umcg-patho group ###################################################################################################################### @@ -1377,21 +1377,21 @@ crontabs: minute: '*/5' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; - moveAndCheckSamplesheets.sh -g umcg-patho -d dat37" + moveAndCheckSamplesheets.sh -g umcg-patho -d dat36" - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; - notifications.sh -g umcg-patho -c -d dat37 -p prm37" + notifications.sh -g umcg-patho -c -d dat36 -p prm36" - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. user: umcg-patho-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated']['default'] }}-bare; - copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm37" + copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm36" ###################################################################################################################### # umcg-pr group ###################################################################################################################### @@ -1401,21 +1401,21 @@ crontabs: # minute: '*/5' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; - # moveAndCheckSamplesheets.sh -g umcg-pr -d dat57" + # moveAndCheckSamplesheets.sh -g umcg-pr -d dat56" # - name: NGS_Automated_notifications # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; - # notifications.sh -g umcg-pr -c -d dat57 -p prm57" + # notifications.sh -g umcg-pr -c -d dat56 -p prm56" # - name: NGS_Automated_copyBclDataToPrm_inhouse # Unique ID required to update existing cronjob: do not modify. # user: umcg-pr-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated']['default'] }}-bare; - # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm57" + # copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm56" ###################################################################################################################### # umcg-lab group ###################################################################################################################### diff --git a/group_vars/wingedhelix_cluster/vars.yml b/group_vars/wingedhelix_cluster/vars.yml index f3a22bd..767a933 100644 --- a/group_vars/wingedhelix_cluster/vars.yml +++ b/group_vars/wingedhelix_cluster/vars.yml @@ -477,7 +477,7 @@ group_notification_targets: # # umcg-lab group # ###################################################################################################################### # - group: umcg-lab - # lfs: tmp06 + # lfs: tmp07 # user: umcg-lab-ateambot # type: notification_webhooks # analysis_phases: [moveSequencingData] From 51c09087c016596d7da9ee20edd9ac967f990b26 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 24 Jan 2025 10:29:21 +0100 Subject: [PATCH 4/6] Update group_vars/betabarrel_cluster/vars.yml --- group_vars/betabarrel_cluster/vars.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/group_vars/betabarrel_cluster/vars.yml b/group_vars/betabarrel_cluster/vars.yml index 2353cca..1c711a7 100644 --- a/group_vars/betabarrel_cluster/vars.yml +++ b/group_vars/betabarrel_cluster/vars.yml @@ -472,9 +472,9 @@ group_notification_targets: # analysis_phases: [copyBclDataToPrm] # notification_target: hpc-helpdesk_and_pr # machines: "{{ groups['chaperone'] }}" - # ###################################################################################################################### - # # umcg-lab group - # ###################################################################################################################### + ###################################################################################################################### + # umcg-lab group + ###################################################################################################################### - group: umcg-lab lfs: tmp05 user: umcg-lab-ateambot From dbb794590e6026936fa0def030c752a7207e116a Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 24 Jan 2025 10:35:27 +0100 Subject: [PATCH 5/6] update ip address nanopore --- group_vars/betabarrel_cluster/vars.yml | 11 +++++++++-- group_vars/copperfist_cluster/vars.yml | 11 +++++++++-- group_vars/wingedhelix_cluster/vars.yml | 11 +++++++++-- 3 files changed, 27 insertions(+), 6 deletions(-) diff --git a/group_vars/betabarrel_cluster/vars.yml b/group_vars/betabarrel_cluster/vars.yml index 2353cca..744263f 100644 --- a/group_vars/betabarrel_cluster/vars.yml +++ b/group_vars/betabarrel_cluster/vars.yml @@ -991,13 +991,20 @@ crontabs: module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-gd" ##### Nanopore ##### - # - name: NGS_Automated_copyRawNanoporeDataToPrm # Unique ID required to update existing cronjob: do not modify. + # - name: NGS_Automated_copyRawNanoporeDataToPrm_10 # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 10.73.57.10" + # - name: NGS_Automated_copyRawNanoporeDataToPrm_11 # Unique ID required to update existing cronjob: do not modify. # user: umcg-gd-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; - # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 145.39.79.24" + # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 10.73.57.11" # - name: NGS_Automated_copyRawNanoporeDataToTmp # Unique ID required to update existing cronjob: do not modify. # user: umcg-gd-dm # machines: "{{ groups['chaperone'] | default([]) }}" diff --git a/group_vars/copperfist_cluster/vars.yml b/group_vars/copperfist_cluster/vars.yml index 125b1ed..076a846 100644 --- a/group_vars/copperfist_cluster/vars.yml +++ b/group_vars/copperfist_cluster/vars.yml @@ -989,13 +989,20 @@ crontabs: module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-gd" ##### Nanopore ##### - # - name: NGS_Automated_copyRawNanoporeDataToPrm # Unique ID required to update existing cronjob: do not modify. + # - name: NGS_Automated_copyRawNanoporeDataToPrm_10 # Unique ID required to update existing cronjob: do not modify. + # user: umcg-gd-dm + # machines: "{{ groups['chaperone'] | default([]) }}" + # minute: '*/10' + # job: /bin/bash -c "{{ configure_env_in_cronjob }}; + # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 10.73.57.10" + # - name: NGS_Automated_copyRawNanoporeDataToPrm_11 # Unique ID required to update existing cronjob: do not modify. # user: umcg-gd-dm # machines: "{{ groups['chaperone'] | default([]) }}" # minute: '*/10' # job: /bin/bash -c "{{ configure_env_in_cronjob }}; # module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; - # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 145.39.79.24" + # copyRawNanoporeDataToPrm.sh -g umcg-gd -r 10.73.57.11" # - name: NGS_Automated_copyRawNanoporeDataToTmp # Unique ID required to update existing cronjob: do not modify. # user: umcg-gd-dm # machines: "{{ groups['chaperone'] | default([]) }}" diff --git a/group_vars/wingedhelix_cluster/vars.yml b/group_vars/wingedhelix_cluster/vars.yml index 767a933..a1363f6 100644 --- a/group_vars/wingedhelix_cluster/vars.yml +++ b/group_vars/wingedhelix_cluster/vars.yml @@ -990,13 +990,20 @@ crontabs: module load ConcordanceCheck/{{ group_module_versions['umcg-gd']['ConcordanceCheck'] }}; cleanup.sh -g umcg-gd" ##### Nanopore ##### - - name: NGS_Automated_copyRawNanoporeDataToPrm # Unique ID required to update existing cronjob: do not modify. + - name: NGS_Automated_copyRawNanoporeDataToPrm_10 # Unique ID required to update existing cronjob: do not modify. + user: umcg-gd-dm + machines: "{{ groups['chaperone'] | default([]) }}" + minute: '*/10' + job: /bin/bash -c "{{ configure_env_in_cronjob }}; + module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; + copyRawNanoporeDataToPrm.sh -g umcg-gd -r 10.73.57.10" + - name: NGS_Automated_copyRawNanoporeDataToPrm_11 # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" minute: '*/10' job: /bin/bash -c "{{ configure_env_in_cronjob }}; module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated']['default'] }}-bare; - copyRawNanoporeDataToPrm.sh -g umcg-gd -r 145.39.79.24" + copyRawNanoporeDataToPrm.sh -g umcg-gd -r 10.73.57.11" - name: NGS_Automated_copyRawNanoporeDataToTmp # Unique ID required to update existing cronjob: do not modify. user: umcg-gd-dm machines: "{{ groups['chaperone'] | default([]) }}" From 5b83ef71ef37e298696a18786c3017f7adbee979 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 24 Jan 2025 10:45:04 +0100 Subject: [PATCH 6/6] Update group_vars/copperfist_cluster/vars.yml --- group_vars/copperfist_cluster/vars.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/group_vars/copperfist_cluster/vars.yml b/group_vars/copperfist_cluster/vars.yml index cbe0f87..57840e6 100644 --- a/group_vars/copperfist_cluster/vars.yml +++ b/group_vars/copperfist_cluster/vars.yml @@ -472,9 +472,9 @@ group_notification_targets: # analysis_phases: [copyBclDataToPrm] # notification_target: hpc-helpdesk_and_pr # machines: "{{ groups['chaperone'] }}" - # ###################################################################################################################### - # # umcg-lab group - # ###################################################################################################################### + ###################################################################################################################### + # umcg-lab group + ###################################################################################################################### - group: umcg-lab lfs: tmp06 user: umcg-lab-ateambot