From 84f34cf4fe307f7c9d9bfbf5ee4cb593af5d92e6 Mon Sep 17 00:00:00 2001 From: JohannesKersting Date: Fri, 1 Dec 2023 10:59:20 +0100 Subject: [PATCH 1/4] created institutional nextflow profile for DaiSyBio --- .github/workflows/main.yml | 1 + README.md | 1 + conf/daisybio.config | 31 +++++++++++++++++++++++++++++++ docs/daisybio.md | 9 +++++++++ nfcore_custom.config | 1 + 5 files changed, 43 insertions(+) create mode 100644 conf/daisybio.config create mode 100644 docs/daisybio.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f6b5e2968..a841696ce 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -55,6 +55,7 @@ jobs: - "crg" - "crick" - "crukmi" + - "daisybio" - "denbi_qbic" - "dkfz" - "ebc" diff --git a/README.md b/README.md index 9d303173d..c1aeda540 100644 --- a/README.md +++ b/README.md @@ -113,6 +113,7 @@ Currently documentation is available for the following systems: - [CRICK](docs/crick.md) - [Cancer Research UK Manchester Institute](docs/crukmi.md) - [CZBIOHUB_AWS](docs/czbiohub.md) +- [DaiSyBio](docs/daisybio.md) - [DENBI_QBIC](docs/denbi_qbic.md) - [DKFZ](docs/dkfz.md) - [EBC](docs/ebc.md) diff --git a/conf/daisybio.config b/conf/daisybio.config new file mode 100644 index 000000000..2ca1cab8a --- /dev/null +++ b/conf/daisybio.config @@ -0,0 +1,31 @@ +params { + config_profile_description = 'DaiSyBio cluster profile provided by nf-core/configs.' + config_profile_contact = 'Johannes Kersting (Johannes Kersting)' + config_profile_url = 'https://biomedical-big-data.de/' + max_memory = 1.TB + max_cpus = 120 + max_time = 96.h + igenomes_base = '/nfs/data/references/igenomes' +} + +process { + executor = 'slurm' + queue = 'shared-cpu' + maxRetries = 2 +} + +executor { + queueSize = 30 + submitRateLimit = '10 sec' +} + +singularity { + cacheDir = '/nfs/scratch/singularity_cache' +} + +apptainer { + cacheDir = '/nfs/scratch/apptainer_cache' +} + + + diff --git a/docs/daisybio.md b/docs/daisybio.md new file mode 100644 index 000000000..16ba57bd7 --- /dev/null +++ b/docs/daisybio.md @@ -0,0 +1,9 @@ +# nf-core/configs: DaiSyBio + + +To use the DaiSyBio profile, run a nf-core pipeline with `-profile DaiSyBio,`. + +This will automatically download and apply ['daisybio.config'](../conf/daisybio.config) as a nextflow config file. + +The config file will set slurm as a scheduler for the compute cluster, define max resources, and specify cache locations for singularity, apptainer, and iGenomes. +Pipeline specific parameters still need to be configured manually. diff --git a/nfcore_custom.config b/nfcore_custom.config index 52fb3b51b..d61a328b7 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -37,6 +37,7 @@ profiles { crick { includeConfig "${params.custom_config_base}/conf/crick.config" } crukmi { includeConfig "${params.custom_config_base}/conf/crukmi.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } + daisybio { includeConfig "${params.custom_config_base}/conf/daisybio.config" } denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" } dkfz { includeConfig "${params.custom_config_base}/conf/dkfz.config" } ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" } From 45bd81d2ba4329b37238245a31f67aad2639311c Mon Sep 17 00:00:00 2001 From: JohannesKersting Date: Fri, 1 Dec 2023 11:40:01 +0100 Subject: [PATCH 2/4] updated docs --- docs/daisybio.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/daisybio.md b/docs/daisybio.md index 16ba57bd7..223179366 100644 --- a/docs/daisybio.md +++ b/docs/daisybio.md @@ -7,3 +7,5 @@ This will automatically download and apply ['daisybio.config'](../conf/daisybio. The config file will set slurm as a scheduler for the compute cluster, define max resources, and specify cache locations for singularity, apptainer, and iGenomes. Pipeline specific parameters still need to be configured manually. + +Singularity and apptainer are currently only installed on the exbio nodes. In order to use them, you can either install singularity/apptainer in a conda environment and execute nextflow inside the environment, or limit the queue to exbio nodes with `-process.queue exbio-cpu` From a43e24ea8e6a9f08d655d8e393ee5c86e48e7328 Mon Sep 17 00:00:00 2001 From: JohannesKersting Date: Fri, 1 Dec 2023 12:06:03 +0100 Subject: [PATCH 3/4] prettier linting --- docs/daisybio.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/daisybio.md b/docs/daisybio.md index 223179366..338f100a6 100644 --- a/docs/daisybio.md +++ b/docs/daisybio.md @@ -1,7 +1,6 @@ # nf-core/configs: DaiSyBio - -To use the DaiSyBio profile, run a nf-core pipeline with `-profile DaiSyBio,`. +To use the DaiSyBio profile, run a nf-core pipeline with `-profile DaiSyBio,`. This will automatically download and apply ['daisybio.config'](../conf/daisybio.config) as a nextflow config file. From 1229149bf0815a48561945d9b91f5c811363b381 Mon Sep 17 00:00:00 2001 From: JohannesKersting <66471005+JohannesKersting@users.noreply.github.com> Date: Fri, 1 Dec 2023 15:43:10 +0100 Subject: [PATCH 4/4] Update docs/daisybio.md Co-authored-by: James A. Fellows Yates --- docs/daisybio.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/daisybio.md b/docs/daisybio.md index 338f100a6..3c7309577 100644 --- a/docs/daisybio.md +++ b/docs/daisybio.md @@ -1,6 +1,6 @@ # nf-core/configs: DaiSyBio -To use the DaiSyBio profile, run a nf-core pipeline with `-profile DaiSyBio,`. +To use the DaiSyBio profile, run a nf-core pipeline with `-profile daisybio,`. This will automatically download and apply ['daisybio.config'](../conf/daisybio.config) as a nextflow config file.