From d80797ce7a10f093897d988edba0949bbb73c2cd Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 23 Dec 2024 15:34:40 +0100 Subject: [PATCH 1/5] Merge changes from main into hotfix (#195) (#382) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Sara Monzón Co-authored-by: Pablo Mata <76519482+Shettland@users.noreply.github.com> Co-authored-by: Víctor López <98259577+victor5lm@users.noreply.github.com> From 29976f8ea32b13e0a599efb3e59875024f4bb7cb Mon Sep 17 00:00:00 2001 From: victor5lm Date: Tue, 24 Dec 2024 11:03:11 +0100 Subject: [PATCH 2/5] Removed middle_obx from config files --- bu_isciii/conf/configuration.json | 2 +- bu_isciii/conf/configuration_dev.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bu_isciii/conf/configuration.json b/bu_isciii/conf/configuration.json index 123441852..95b1d9aa0 100644 --- a/bu_isciii/conf/configuration.json +++ b/bu_isciii/conf/configuration.json @@ -58,7 +58,7 @@ ], "scratch_path": "/scratch/bi/", "srun_settings": { - "--partition": "middle_obx,middle_idx", + "--partition": "middle_idx", "--time": "24:00:00", "--chdir": "/scratch/bi/" } diff --git a/bu_isciii/conf/configuration_dev.json b/bu_isciii/conf/configuration_dev.json index 39d0c483a..94573b6a4 100755 --- a/bu_isciii/conf/configuration_dev.json +++ b/bu_isciii/conf/configuration_dev.json @@ -54,7 +54,7 @@ ], "scratch_path": "tests/scratch/bi/", "srun_settings": { - "--partition": "middle_obx,middle_idx", + "--partition": "middle_idx", "--time": "24:00:00", "--chdir": "tests/scratch/bi/" } From 38032be4bf1bde2a30c8cf16ce0cba4892c04131 Mon Sep 17 00:00:00 2001 From: victor5lm Date: Tue, 24 Dec 2024 11:03:28 +0100 Subject: [PATCH 3/5] Replaced /data/bi by /data/ucct/bi where necessary --- .../ANALYSIS01_FLU_IRMA/01-preproQC/lablog | 2 +- .../ANALYSIS01_FLU_IRMA/03-procQC/lablog | 2 +- .../ANALYSIS01_FLU_IRMA/04-irma/lablog | 2 +- .../ANALYSIS/ANALYSIS01_ASSEMBLY/lablog | 2 +- .../blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog | 2 +- .../02-ariba/run/lablog | 2 +- .../02-ariba/summary/lablog | 2 +- .../04-emmtyper/lablog | 2 +- .../ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog | 2 +- .../ANALYSIS01_EXOME/02-postprocessing/lablog | 2 +- .../ANALYSIS01_EXOME/03-annotation/lablog | 6 ++--- .../ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog | 2 +- .../exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog | 2 +- .../ANALYSIS01_EXOME/02-postprocessing/lablog | 2 +- .../ANALYSIS01_EXOME/03-annotation/lablog | 10 ++++---- .../ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog | 2 +- .../ANALYSIS/ANALYSIS01_EXOME/lablog | 2 +- .../ANALYSIS01_OUTBREAK/01-preproQC/lablog | 2 +- .../ANALYSIS01_OUTBREAK/03-procQC/lablog | 2 +- .../ANALYSIS01_OUTBREAK/04-Alignment/lablog | 2 +- .../ANALYSIS01_OUTBREAK/05-mark_dups/lablog | 2 +- .../ANALYSIS01_OUTBREAK/06-freebayes/lablog | 2 +- .../ANALYSIS01_OUTBREAK/07-snphylo/lablog | 2 +- .../ANALYSIS01_OUTBREAK/08-iqtree/lablog | 2 +- .../ANALYSIS01_OUTBREAK/99-stats/lablog | 2 +- .../ANALYSIS/ANALYSIS02_MET/99-stats/lablog | 2 +- .../ANALYSIS/ANALYSIS02_MET/lablog | 2 +- .../ANALYSIS01_RBPANEL/01-fastQC/lablog | 2 +- .../ANALYSIS01_RBPANEL/03-preprocQC/lablog | 2 +- .../ANALYSIS01_RBPANEL/04-mapping/lablog | 2 +- .../ANALYSIS01_RBPANEL/05-samtools/lablog | 2 +- .../ANALYSIS01_RBPANEL/06-VarScan/lablog | 2 +- .../ANALYSIS01_RBPANEL/07-annotation/lablog | 2 +- .../ANALYSIS01_RBPANEL/99-stats/lablog | 2 +- .../ANALYSIS/ANALYSIS01_TAXPROFILER/lablog | 2 +- .../ANALYSIS02_MAG_TAXONOMICS/99-stats/lablog | 2 +- .../ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/lablog | 2 +- .../mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog | 2 +- .../ANALYSIS01_MTBSEQ/02-kmerfinder/lablog | 2 +- .../ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog | 2 +- .../ANALYSIS/ANALYSIS02_PLASMIDID/lablog | 2 +- .../02-differential_expression/lablog | 2 +- .../ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog | 2 +- .../ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog | 2 +- .../ANALYSIS01_SNIPPY/01-fastqc/lablog | 2 +- .../ANALYSIS01_SNIPPY/03-preprocQC/lablog | 2 +- .../ANALYSIS01_SNIPPY/04-snippy/lablog | 2 +- .../ANALYSIS01_SNIPPY/05-iqtree/lablog | 2 +- .../ANALYSIS01_SNIPPY/99-stats/lablog | 2 +- .../viralrecon/ANALYSIS/lablog_viralrecon | 2 +- .../02-postprocessing/lablog | 2 +- .../ANALYSIS01_GENOME/03-annotation/lablog | 24 +++++++++---------- .../ANALYSIS01_GENOME/99-stats/lablog | 2 +- .../wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog | 2 +- .../20221205_ANALYSIS01_ASSEMBLY/lablog | 2 +- .../20221205_ANALYSIS01_ASSEMBLY/lablog | 2 +- .../lablog | 2 +- .../ANALYSIS/20221205_ANALYSIS03_MAG/lablog | 2 +- .../ANALYSIS/20221207_ANALYSIS04_BLAST/lablog | 2 +- .../ANALYSIS/lablog | 2 +- .../ANALYSIS/ANALYSIS01_ASSEMBLY/lablog | 2 +- 61 files changed, 78 insertions(+), 78 deletions(-) diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/01-preproQC/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/01-preproQC/lablog index a496affd5..570ebed60 100644 --- a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/01-preproQC/lablog +++ b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/01-preproQC/lablog @@ -2,6 +2,6 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --cpus-per-task 8 --time 01:00:00 --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ -B /srv/fastq_repo/ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../00-reads/"$in"_R1.fastq.gz ${scratch_dir}/../00-reads/"$in"_R2.fastq.gz &"; done > _01_rawfastqc.sh diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/03-procQC/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/03-procQC/lablog index 2bfd95ba1..686602918 100644 --- a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/03-procQC/lablog +++ b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/03-procQC/lablog @@ -2,6 +2,6 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz &"; done > _01_rawfastqc.sh diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog index b6196b72b..fcf827589 100644 --- a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog +++ b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog @@ -3,7 +3,7 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/ucct/bi/pipelines/flu-amd/flu-amd-1.1.4/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma.sh diff --git a/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog b/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog index 5aa86c1a4..f9c13f25a 100644 --- a/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog +++ b/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog @@ -92,7 +92,7 @@ cat samples_id.txt | while read in; do fi done >> samplesheet.csv -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < assembly.sbatch #!/bin/sh diff --git a/bu_isciii/templates/blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog b/bu_isciii/templates/blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog index cf92cc65e..3f72f71c7 100644 --- a/bu_isciii/templates/blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog +++ b/bu_isciii/templates/blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir logs # Location of assemblies to a variable so it only has to be changed here diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog index f31e7ae2f..36f1038a5 100644 --- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog +++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog @@ -1,7 +1,7 @@ # module load singularity mkdir logs -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') downloaded_ref=$(find ../../../../REFERENCES/ -type d -name 'ref_db') # Cartesian product of the two files to avoid double looping diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog index baf447a80..697e121c0 100644 --- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog +++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog @@ -1,7 +1,7 @@ # module load singularity mkdir -p logs -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') # Ariba summarise data from several runs. View the results in Phandango by dragging and dropping the files out.summary.phandango.tre and out.summary.phandango.csv into the Phandago window. # Explanation: diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog index fd126538b..1e5138afe 100644 --- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog +++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog @@ -12,7 +12,7 @@ ASSEMBLY_LIST=fasta_inputs/assembly_file_list.txt # Get the number of files num_files=$(wc -l < $ASSEMBLY_LIST) -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") # STEP 1: Set up jobarray to unzip fasta files cat < _00_unzip_jobarray.sbatch diff --git a/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog b/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog index d74a4f22e..185928e92 100644 --- a/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog +++ b/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog @@ -1,4 +1,4 @@ -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") # module load singularity diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog index 0c971e16e..bdb99167c 100644 --- a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog +++ b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog @@ -2,7 +2,7 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir -p logs diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog index 45b655319..e03a09947 100644 --- a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog +++ b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog @@ -1,7 +1,7 @@ # module load singularity # module load Java/17.0.2.lua R/4.2.1 -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37/dbNSFP_ENSG_gene_GRCh37.txt . mkdir -p vep @@ -39,9 +39,9 @@ echo "srun --partition short_idx --time 2:00:00 --chdir ${scratch_dir} --output echo 'grep -P "(HIGH|MODERATE)" ./variants_annot_all.tab > ./variants_annot_highModerate.tab ' > _05_conseq_filtering.sh # 9. Running exomiser -vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped) -output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") sed -i "s|VCF_FILE|${vcf_file}|g" ./exomiser_configfile.yml sed -i "s|PROBAND|${proband}|g" ./exomiser_configfile.yml diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog index f78ff9400..55f2c56d4 100644 --- a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog +++ b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir logs cat ../samples_id.txt | xargs -I @@ echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir ${scratch_dir} --output logs/PICARDHSMETRICS.@@.%j.log --job-name PICARDHSMETRICS singularity exec -B ${scratch_dir}/../../../ -B /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard CollectHsMetrics -R /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37_decoy.fasta -BI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -TI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -I ${scratch_dir}/../01-sarek/preprocessing/recalibrated/@@/@@.recal.cram -O ${scratch_dir}/@@_hsMetrics.out -VALIDATION_STRINGENCY LENIENT &" > _01_picardHsMetrics.sh diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog index e8ca5a5b3..83ed5bbba 100755 --- a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog +++ b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog @@ -14,7 +14,7 @@ done < ./samples_id.txt mkdir -p 02-postprocessing 03-annotation 99-stats -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < sarek.sbatch #!/bin/sh diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog index e366b6d35..0bf87c35f 100644 --- a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog +++ b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog @@ -3,7 +3,7 @@ # Lablog to apply variant filters to combined GVCFs generated by SAREK (HaplotypeCaller) -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir -p logs diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog index 5017cb561..79bde1ca1 100644 --- a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog +++ b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog @@ -1,7 +1,7 @@ # module load singularity # module load Java/17.0.2.lua R/4.2.1 -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37-4.3/dbNSFP_ENSG_gene_GRCh37.txt ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37-4.3/dbNSFP_ENSG_plugin_hg19.txt @@ -58,11 +58,11 @@ echo "rm variants_annot_filterAF.tab" >> aux_03_awk.sh #------------------------------------------------------------------------------------------------------- # 9. Running exomiser -vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") -ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") +ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped) -bed_file=$(realpath ../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37_mod.bed | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") -output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +bed_file=$(realpath ../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37_mod.bed | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") +output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") sed -i "s|VCF_FILE|${vcf_file}|g" ./exomiser_configfile.yml sed -i "s|PED_FILE|${ped_file}|g" ./exomiser_configfile.yml diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog index e3fc7690e..9739b1c7a 100644 --- a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog +++ b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir logs cat ../samples_id.txt | xargs -I @@ echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir ${scratch_dir} --output logs/PICARDHSMETRICS.@@.%j.log --job-name PICARDHSMETRICS singularity exec -B ${scratch_dir}/../../../ -B /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/ /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard CollectHsMetrics -R /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37_decoy.fasta -BI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -TI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -I ${scratch_dir}/../01-sarek/preprocessing/recalibrated/@@/@@.recal.cram -O ${scratch_dir}/@@_hsMetrics.out -VALIDATION_STRINGENCY LENIENT &" > _01_picardHsMetrics.sh diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog index 2f3513917..ad3161803 100755 --- a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog +++ b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog @@ -28,7 +28,7 @@ echo -e "patient,sex,status,sample,lane,fastq_1,fastq_2" > samplesheet.csv cat samples_id.txt | xargs -I % echo -e "%,XY,0,%,1,00-reads/%_R1.fastq.gz,00-reads/%_R2.fastq.gz" >> samplesheet.csv mkdir -p 02-postprocessing 03-annotation 99-stats -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < sarek.sbatch #!/bin/sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/01-preproQC/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/01-preproQC/lablog index a496affd5..570ebed60 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/01-preproQC/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/01-preproQC/lablog @@ -2,6 +2,6 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --cpus-per-task 8 --time 01:00:00 --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ -B /srv/fastq_repo/ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../00-reads/"$in"_R1.fastq.gz ${scratch_dir}/../00-reads/"$in"_R2.fastq.gz &"; done > _01_rawfastqc.sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/03-procQC/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/03-procQC/lablog index c860c2561..16b8e75c4 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/03-procQC/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/03-procQC/lablog @@ -2,6 +2,6 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz &"; done > _01_preprofastqc.sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/04-Alignment/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/04-Alignment/lablog index d52189714..f18243d73 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/04-Alignment/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/04-Alignment/lablog @@ -2,7 +2,7 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --chdir $scratch_dir --output logs/BWAMEM.${in}.%j.log --cpus-per-task 20 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/bwa:0.7.17--he4a0461_11 bwa mem -t 20 REFERENCE_GENOME ${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz -o ${scratch_dir}/${in}/${in}.sam &"; done >> _01_bwamem.sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/05-mark_dups/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/05-mark_dups/lablog index edd952a14..d553cb1a0 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/05-mark_dups/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/05-mark_dups/lablog @@ -2,7 +2,7 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do mkdir ${in}; echo "srun --partition short_idx --chdir $scratch_dir --output logs/PICARD_DUPLICATES.${in}.%j.log --mem 251346M --cpus-per-task 20 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard MarkDuplicates ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=false INPUT=${scratch_dir}/../04-Alignment/${in}/${in}_sorted_rg.bam OUTPUT=${scratch_dir}/${in}/${in}_woduplicates.bam METRICS_FILE=${scratch_dir}/${in}/${in}_duplicates.stats TMP_DIR=${scratch_dir}/../../../TMP/${in} &"; done > _01_picard_dups.sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/06-freebayes/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/06-freebayes/lablog index 6dde10961..649f633f7 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/06-freebayes/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/06-freebayes/lablog @@ -2,7 +2,7 @@ mkdir -p logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < freebayes.sbatch #!/bin/sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/07-snphylo/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/07-snphylo/lablog index 34cc7337b..a05c15b6a 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/07-snphylo/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/07-snphylo/lablog @@ -1,6 +1,6 @@ # module load R/4.1.3 -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir logs diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/08-iqtree/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/08-iqtree/lablog index 3eb5954ae..0e308a0c1 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/08-iqtree/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/08-iqtree/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir log echo "srun --chdir ${scratch_dir} --output logs/IQTREEMFP.%j.log --job-name IQTREEMFP --cpus-per-task 20 --mem 5G --partition short_idx --time 00:30:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../07-snphylo/snphylo.output.fasta -m MFP &" > _00_iqtreemfp.sh echo "srun --chdir ${scratch_dir} --output logs/IQTREEFULLALIGN.%j.log --job-name IQTREEFULLALIGN --cpus-per-task 20 --mem 15G --partition short_idx --time 08:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../07-snphylo/snphylo.output.fasta -m PMB+F+R2 -T 20 -B 1000 -pre phylo.iqtree.bootstrap &" > _01_iqtreeall.sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/99-stats/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/99-stats/lablog index 98989b223..476033697 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/99-stats/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/99-stats/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir -p logs mkdir samtools_flagstats diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/lablog index 74f1c4941..aa6cc2d72 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/lablog @@ -2,7 +2,7 @@ cat ../../samples_id.txt | while read in; do ln -s ../*_mag/Taxonomy/kraken2/${in}/kraken2_report.txt ./${in}_kraken2_report.txt; done -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < multiqc.sbatch #!/bin/sh diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog index fc3789a6a..69dee18e6 100644 --- a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog +++ b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog @@ -3,7 +3,7 @@ ln -s ../samples_id.txt . #module load Nextflow singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < mag.sbatch #!/bin/sh diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/01-fastQC/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/01-fastQC/lablog index a334d1e89..88683bd09 100644 --- a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/01-fastQC/lablog +++ b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/01-fastQC/lablog @@ -1,5 +1,5 @@ # module load singularity -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir logs cat ../samples_id.txt | xargs -I @@ echo "mkdir @@;srun --chdir ${scratch_dir} --output logs/FASTQC.@@.%j.log --job-name FASTQC --cpus-per-task 8 --mem 8192 --partition short_idx --time 02:00:00 singularity exec -B ${scratch_dir}/../../../ -B /srv/fastq_repo/ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/@@ --nogroup -t 8 -k 8 ${scratch_dir}/../00-reads/@@_R1.fastq.gz ${scratch_dir}/../00-reads/@@_R2.fastq.gz &" >> _01_fastqc.sh diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/03-preprocQC/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/03-preprocQC/lablog index 4be9b022a..de8fb0666 100644 --- a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/03-preprocQC/lablog +++ b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/03-preprocQC/lablog @@ -1,5 +1,5 @@ # module load singularity -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir logs cat ../samples_id.txt | xargs -I @@ echo "mkdir @@;srun --chdir ${scratch_dir} --output logs/FASTQC.@@.%j.log --job-name FASTQC --cpus-per-task 8 --mem 8192 --partition short_idx --time 02:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/@@ --nogroup -t 8 -k 8 ${scratch_dir}/../02-preprocessing/@@/@@_R1_filtered.fastq ${scratch_dir}/../02-preprocessing/@@/@@_R2_filtered.fastq &" >> _01_fastqc.sh diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/04-mapping/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/04-mapping/lablog index 908810446..779c1e388 100644 --- a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/04-mapping/lablog +++ b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/04-mapping/lablog @@ -2,7 +2,7 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") echo "Use bash lablog ../samples_id.txt" diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/05-samtools/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/05-samtools/lablog index 04e55c81b..8490cc5d0 100644 --- a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/05-samtools/lablog +++ b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/05-samtools/lablog @@ -2,7 +2,7 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") echo "Use bash lablog ../samples_id.txt" diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/06-VarScan/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/06-VarScan/lablog index f47c75f19..cc52419ff 100644 --- a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/06-VarScan/lablog +++ b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/06-VarScan/lablog @@ -2,7 +2,7 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") echo "Use bash lablog ../samples_id.txt" diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog index 1640cd2f5..65f7cce0d 100644 --- a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog +++ b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir logs echo "Use bash lablog ../samples_id.txt" diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/lablog index 1ad62c614..9091852be 100644 --- a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/lablog +++ b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir logs cat ../samples_id.txt | xargs -I @@ echo "srun --chdir ${scratch_dir} --output logs/PICARD.@@.%j.log --job-name PICARD --cpus-per-task 1 --mem 8192 --partition short_idx --time 02:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard CollectHsMetrics -BI ${scratch_dir}/../../../REFERENCES/idt_rb1_panel_20221123.interval_list -TI ${scratch_dir}/../../../REFERENCES/idt_rb1_panel_20221123.interval_list -I ${scratch_dir}/../04-mapping/@@/@@_sorted.bam -O ${scratch_dir}/@@_hsMetrics.out -VALIDATION_STRINGENCY 'LENIENT' &" > _01_picardHsMetrics.sh diff --git a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog index d08d846ff..879010d8d 100644 --- a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog +++ b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog @@ -51,7 +51,7 @@ cat samples_id.txt | while read in; do echo "${in},run1,ILLUMINA,00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz," done >> samplesheet.csv -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") # slurm sbatch file setup cat < taxprofiler.sbatch diff --git a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/99-stats/lablog b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/99-stats/lablog index 94231de1a..a9daa731f 100644 --- a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/99-stats/lablog +++ b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/99-stats/lablog @@ -2,7 +2,7 @@ cat ../../samples_id.txt | while read in; do ln -s ../*_mag/Taxonomy/kraken2/${in}/${in}.kraken2_report.txt .; done -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < multiqc.sbatch #!/bin/sh diff --git a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/lablog b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/lablog index b641a1d25..6dddb048c 100644 --- a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/lablog +++ b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/lablog @@ -11,7 +11,7 @@ done >> samplesheet.csv #module load Nextflow #module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < mag.sbatch #!/bin/sh diff --git a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog index 754af025c..1f57ae768 100644 --- a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog +++ b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog @@ -8,7 +8,7 @@ cat samples_id.txt | while read in; do echo "${in},,00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz," done >> samplesheet.csv -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < mag_all.sbatch #!/bin/sh diff --git a/bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/02-kmerfinder/lablog b/bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/02-kmerfinder/lablog index cbc97034f..f94fe55f2 100644 --- a/bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/02-kmerfinder/lablog +++ b/bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/02-kmerfinder/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir logs diff --git a/bu_isciii/templates/pikavirus/ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog b/bu_isciii/templates/pikavirus/ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog index d722b0b99..3074c0bcd 100644 --- a/bu_isciii/templates/pikavirus/ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog +++ b/bu_isciii/templates/pikavirus/ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog @@ -6,7 +6,7 @@ echo "sample,fastq_1,fastq_2" > samplesheet.csv cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz"; done >> samplesheet.csv -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < pikavirus.sbatch #!/bin/sh diff --git a/bu_isciii/templates/plasmidid/ANALYSIS/ANALYSIS02_PLASMIDID/lablog b/bu_isciii/templates/plasmidid/ANALYSIS/ANALYSIS02_PLASMIDID/lablog index 4e45d1ac0..92e188605 100644 --- a/bu_isciii/templates/plasmidid/ANALYSIS/ANALYSIS02_PLASMIDID/lablog +++ b/bu_isciii/templates/plasmidid/ANALYSIS/ANALYSIS02_PLASMIDID/lablog @@ -1,7 +1,7 @@ # module load singularity mkdir logs -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') ln -s ../samples_id.txt . cat ../samples_id.txt | xargs -I @@ echo "srun --chdir $scratch_dir --output logs/PLASMIDID.@@.%j.log --job-name PLASMIDID_@@ --partition short_idx --time 05:00:00 env - PATH="$PATH" singularity exec --bind /data/ucct/bi/references/ --bind ${scratch_dir} --bind ${scratch_dir}/../../ /data/ucct/bi/pipelines/singularity-images/depot.galaxyproject.org-singularity-plasmidid-1.6.5--hdfd78af_0.img plasmidID -1 ${scratch_dir}/../*ASSEMBLY/01-processing/fastp/@@_1.fastp.fastq.gz -2 ${scratch_dir}/../*ASSEMBLY/01-processing/fastp/@@_2.fastp.fastq.gz -d /data/ucct/bi/references/plasmidID/plasmid_ddbb/20200203/20200203_plasmids.fasta -s @@ -c ${scratch_dir}/../*ASSEMBLY/03-assembly/unicycler/@@.fasta -a ${scratch_dir}/plasmidID_annotation_config_file.txt --no-trim -o ${scratch_dir} &" > _01_plasmidID.sh diff --git a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/lablog b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/lablog index f6694c137..62ed7b42a 100644 --- a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/lablog +++ b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/lablog @@ -3,5 +3,5 @@ COUNTS=$(find ../*rnaseq/ -maxdepth 0 -type d) cat comparatives.txt | tr '\t' '_' | while read in; do mkdir ${in}; cp differential_expression.R ${in}/ ; done cat comparatives.txt | while read in; do arr=($in); echo "mkdir logs" > ${arr[0]}_${arr[1]}_${arr[2]}/lablog; done -cat comparatives.txt | while read in; do arr=($in); echo 'scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")' >> ${arr[0]}_${arr[1]}_${arr[2]}/lablog; done +cat comparatives.txt | while read in; do arr=($in); echo 'scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")' >> ${arr[0]}_${arr[1]}_${arr[2]}/lablog; done cat comparatives.txt | sed 's/-/,/g' | while read in; do arr=($in); echo "echo \"srun --partition short_idx --chdir \$scratch_dir --output logs/DESEQ2.%j.log Rscript differential_expression.R -r ../${COUNTS} -d 'DEG' -t '${arr[1]}' -c '${arr[2]}' &\" > _01_deseq2.sh" >> ${arr[0]}_${arr[1]}_${arr[2]}/lablog; done diff --git a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog index 168c45fb5..d94351850 100644 --- a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog +++ b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog @@ -5,7 +5,7 @@ cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00 #module load Nextflow singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < rnaseq.sbatch #!/bin/sh diff --git a/bu_isciii/templates/seek_and_destroy/ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog b/bu_isciii/templates/seek_and_destroy/ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog index 68ec350e3..948a4a5c5 100644 --- a/bu_isciii/templates/seek_and_destroy/ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog +++ b/bu_isciii/templates/seek_and_destroy/ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog @@ -7,7 +7,7 @@ ln -s ../samples_id.txt . echo "sample,fastq_1,fastq_2" > samplesheet.csv cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz"; done >> samplesheet.csv -scratch_dir=$(echo $(pwd) | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $(pwd) | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < seek_destroy.sbatch #!/bin/sh diff --git a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/01-fastqc/lablog b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/01-fastqc/lablog index 3ffb0cd3b..9889fb5e9 100644 --- a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/01-fastqc/lablog +++ b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/01-fastqc/lablog @@ -2,6 +2,6 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --cpus-per-task 8 --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ -B /srv/fastq_repo/ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../00-reads/"$in"_R1.fastq.gz ${scratch_dir}/../00-reads/"$in"_R2.fastq.gz &"; done > _01_rawfastqc.sh diff --git a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/03-preprocQC/lablog b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/03-preprocQC/lablog index 938fb2161..7628729cb 100644 --- a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/03-preprocQC/lablog +++ b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/03-preprocQC/lablog @@ -2,6 +2,6 @@ mkdir logs -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --cpus-per-task 8 --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz &"; done > _01_trimmedfastqc.sh diff --git a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog index 071496b97..e9f837feb 100644 --- a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog +++ b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir logs diff --git a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/05-iqtree/lablog b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/05-iqtree/lablog index 756b8b09f..d1efc0934 100644 --- a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/05-iqtree/lablog +++ b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/05-iqtree/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') mkdir logs #echo "srun --chdir ${scratch_dir} --output logs/IQTREEMFP.%j.log --job-name IQTREEMFP --cpus-per-task 20 --mem 5G --partition short_idx --time 00:30:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../04-snippy/phylo.aln -m MFP &" > _00_iqtreemfp.sh echo "srun --chdir ${scratch_dir} --output logs/IQTREEFULLALIGN.%j.log --job-name IQTREEFULLALIGN --cpus-per-task 20 --mem 15G --partition short_idx --time 08:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../04-snippy/phylo.aln -m HKY+F+I -T 20 -B 1000 -pre phylo.iqtree.bootstrap &" > _01_iqtreeall.sh diff --git a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/99-stats/lablog b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/99-stats/lablog index 1739247ee..57caf0d43 100644 --- a/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/99-stats/lablog +++ b/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/99-stats/lablog @@ -2,7 +2,7 @@ ln -s ../../../REFERENCES/*.fna reference.fna mkdir logs -scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g') +scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g') cat ../samples_id.txt | xargs -I % echo "printf '%s\t' %;singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/samtools:1.16.1--h6899075_1 samtools flagstat ${scratch_dir}/../04-snippy/%/snps.bam | grep 'mapped (' | head -n 1 | cut -d '(' -f 2 | cut -d ':' -f 1" | bash | sort -u > mapping_stats.txt diff --git a/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon b/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon index 2a829ba76..6f8c21dc8 100644 --- a/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon +++ b/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon @@ -484,7 +484,7 @@ do echo "ln -s ../00-reads ." > ${FOLDER_NAME}/lablog printf "ln -s ../samples_id.txt .\n\n" >> ${FOLDER_NAME}/lablog printf "#module load Nextflow singularity\n\n" >> ${FOLDER_NAME}/lablog - printf 'scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")\n\n' >> ${FOLDER_NAME}/lablog + printf 'scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")\n\n' >> ${FOLDER_NAME}/lablog cut -f2 ${FOLDER_NAME}/samples_ref.txt | sort -u | while read ref do echo "sample,fastq_1,fastq_2" > ${FOLDER_NAME}/samplesheet_${ref}.csv diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/02-postprocessing/lablog b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/02-postprocessing/lablog index 0c971e16e..bdb99167c 100644 --- a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/02-postprocessing/lablog +++ b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/02-postprocessing/lablog @@ -2,7 +2,7 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir -p logs diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/lablog b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/lablog index 246e919a5..93774e4ab 100644 --- a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/lablog +++ b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/lablog @@ -1,7 +1,7 @@ # module load singularity # module load Java/17.0.2.lua R/4.2.1 -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37-4.3/dbNSFP_ENSG_gene_GRCh37.txt ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37-4.3/dbNSFP_ENSG_plugin_hg19.txt @@ -62,10 +62,10 @@ echo "rm variants_annot_filterAF.tab" >> aux_03_awk.sh ## 7. Running exomiser -vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") -ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") +ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped) -output_folder=$(realpath ./exomiser/exomiser/exomiser | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +output_folder=$(realpath ./exomiser/exomiser/exomiser | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") sed -i "s|VCF_FILE|${vcf_file}|g" ./exomiser_configfile.yml sed -i "s|PED_FILE|${ped_file}|g" ./exomiser_configfile.yml @@ -78,11 +78,11 @@ echo "srun --partition short_idx --mem 350G --time 12:00:00 --chdir /data/ucct/b ## 8. Running exomiser_exome -vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") -ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") +ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped) -bed_file=$(realpath ../../../REFERENCES/exomiser_exome.bed | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") -output_folder=$(realpath ./exomiser/exomiser_exome/exomiser_exome | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +bed_file=$(realpath ../../../REFERENCES/exomiser_exome.bed | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") +output_folder=$(realpath ./exomiser/exomiser_exome/exomiser_exome | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") sed -i "s|VCF_FILE|${vcf_file}|g" ./exomiser_configfile_exome.yml sed -i "s|PED_FILE|${ped_file}|g" ./exomiser_configfile_exome.yml @@ -95,11 +95,11 @@ echo "srun --partition short_idx --mem 350G --time 12:00:00 --chdir /data/ucct/b ## 9. Running exomiser_genes -vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") -ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") +ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped) -bed_file=$(realpath ../../../REFERENCES/exomiser_genes.bed | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") -output_folder=$(realpath ./exomiser/exomiser_genes/exomiser_genes | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +bed_file=$(realpath ../../../REFERENCES/exomiser_genes.bed | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") +output_folder=$(realpath ./exomiser/exomiser_genes/exomiser_genes | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") sed -i "s|VCF_FILE|${vcf_file}|g" ./exomiser_configfile_genes.yml sed -i "s|PED_FILE|${ped_file}|g" ./exomiser_configfile_genes.yml diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/99-stats/lablog b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/99-stats/lablog index 08dc70415..5bc35ea0a 100644 --- a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/99-stats/lablog +++ b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/99-stats/lablog @@ -1,6 +1,6 @@ # module load singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir logs cat ../samples_id.txt | xargs -I @@ echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir ${scratch_dir} --output logs/PICARDHSMETRICS.@@.%j.log --job-name PICARDHSMETRICS singularity exec -B ${scratch_dir}/../../../ -B /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/ /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard CollectHsMetrics -R /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37_decoy.fasta -BI ${scratch_dir}/../../../REFERENCES/exomiser_exome_mod.interval_list -TI ${scratch_dir}/../../../REFERENCES/exomiser_exome_mod.interval_list -I ${scratch_dir}/../01-sarek/preprocessing/recalibrated/@@/@@.recal.cram -O ${scratch_dir}/@@_hsMetrics.out -VALIDATION_STRINGENCY LENIENT &" > _01_picardHsMetrics.sh diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog index 7fbc9ebfd..ec0a546d2 100755 --- a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog +++ b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog @@ -30,7 +30,7 @@ cat samples_id.txt | xargs -I % echo -e "%,XY,0,%,1,00-reads/%_R1.fastq.gz,00-re mkdir -p 02-postprocessing 03-annotation 99-stats -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < sarek.sbatch #!/bin/sh diff --git a/tests/archived/bi/research/20230101_TESTRESEARCHP_smonzon_C/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog b/tests/archived/bi/research/20230101_TESTRESEARCHP_smonzon_C/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog index 0de333a1d..c8e2f5246 100644 --- a/tests/archived/bi/research/20230101_TESTRESEARCHP_smonzon_C/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog +++ b/tests/archived/bi/research/20230101_TESTRESEARCHP_smonzon_C/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog @@ -15,7 +15,7 @@ echo "sample,fastq_1,fastq_2" > samplesheet.csv cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz"; done >> samplesheet.csv #module load Nextflow singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < assembly.sbatch #!/bin/sh diff --git a/tests/archived/bi/services_and_colaborations/CNM/bacteriology/SRVCNM787_20221205_ASSEMBLY315_lherrera_S/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog b/tests/archived/bi/services_and_colaborations/CNM/bacteriology/SRVCNM787_20221205_ASSEMBLY315_lherrera_S/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog index 0de333a1d..c8e2f5246 100644 --- a/tests/archived/bi/services_and_colaborations/CNM/bacteriology/SRVCNM787_20221205_ASSEMBLY315_lherrera_S/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog +++ b/tests/archived/bi/services_and_colaborations/CNM/bacteriology/SRVCNM787_20221205_ASSEMBLY315_lherrera_S/ANALYSIS/20221205_ANALYSIS01_ASSEMBLY/lablog @@ -15,7 +15,7 @@ echo "sample,fastq_1,fastq_2" > samplesheet.csv cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz"; done >> samplesheet.csv #module load Nextflow singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < assembly.sbatch #!/bin/sh diff --git a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS02_METAGENOMIC_HUMAN/lablog b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS02_METAGENOMIC_HUMAN/lablog index 4bb83f62c..9f8c0d980 100644 --- a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS02_METAGENOMIC_HUMAN/lablog +++ b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS02_METAGENOMIC_HUMAN/lablog @@ -3,7 +3,7 @@ ln -s ../samples_id.txt . #module load Nextflow singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < RotavirusA_11segments_viralrecon.sbatch #!/bin/sh diff --git a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS03_MAG/lablog b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS03_MAG/lablog index 78abe5121..160448141 100644 --- a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS03_MAG/lablog +++ b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS03_MAG/lablog @@ -3,7 +3,7 @@ ln -s ../samples_id.txt . #module load Nextflow singularity -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < mag.sbatch #!/bin/sh diff --git a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221207_ANALYSIS04_BLAST/lablog b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221207_ANALYSIS04_BLAST/lablog index 2d817bebc..8cdb52c92 100644 --- a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221207_ANALYSIS04_BLAST/lablog +++ b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221207_ANALYSIS04_BLAST/lablog @@ -1,5 +1,5 @@ #module load BLAST+/2.11.0-gompi-2020b -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") mkdir logs diff --git a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/lablog b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/lablog index 0fc44fd73..0fd93a108 100644 --- a/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/lablog +++ b/tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/lablog @@ -16,7 +16,7 @@ do printf "ln -s ../samples_id.txt .\n\n" >> ${FOLDER_NAME}/lablog echo "#module load Nextflow singularity" >> ${FOLDER_NAME}/lablog echo "" >> ${FOLDER_NAME}/lablog - printf 'scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")\n\n' >> ${FOLDER_NAME}/lablog + printf 'scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")\n\n' >> ${FOLDER_NAME}/lablog cut -f2 ${FOLDER_NAME}/samples_ref.txt | sort -u | while read ref do echo "sample,fastq_1,fastq_2" > ${FOLDER_NAME}/samplesheet_${ref}.csv diff --git a/tests/data/bi/services_and_colaborations/CNM/bacteriology/SRVCNM983_20240228_TEST001_bioinfoadm_S/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog b/tests/data/bi/services_and_colaborations/CNM/bacteriology/SRVCNM983_20240228_TEST001_bioinfoadm_S/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog index f96f271b0..5e153a1dd 100644 --- a/tests/data/bi/services_and_colaborations/CNM/bacteriology/SRVCNM983_20240228_TEST001_bioinfoadm_S/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog +++ b/tests/data/bi/services_and_colaborations/CNM/bacteriology/SRVCNM983_20240228_TEST001_bioinfoadm_S/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog @@ -92,7 +92,7 @@ cat samples_id.txt | while read in; do fi done >> samplesheet.csv -scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") +scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g") cat < assembly.sbatch #!/bin/sh From a26df51954af6d396fd8a534358d0ac909e9ab0b Mon Sep 17 00:00:00 2001 From: victor5lm Date: Tue, 24 Dec 2024 11:14:23 +0100 Subject: [PATCH 4/5] Updated CHANGELOG.md --- CHANGELOG.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 154251f8e..5a0fd384b 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,29 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [2.2.4dev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.4 + +### Credits + +- [Victor Lopez](https://github.com/victor5lm) + +### Template fixes and updates + +- Replaced /data/bi/ by /data/ucct/bi where necessary [#385](https://github.com/BU-ISCIII/buisciii-tools/pull/385). +- Removed middle_obx from config files [#385](https://github.com/BU-ISCIII/buisciii-tools/pull/385). + +### Modules + +#### Added enhancements + +#### Fixes + +#### Changed + +#### Removed + +### Requirements + ## [2.X.Xhot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.3 ### Credits From f8774f339f15cc40f4f415cf8fe1fd5fc341be9f Mon Sep 17 00:00:00 2001 From: victor5lm Date: Fri, 27 Dec 2024 10:55:08 +0100 Subject: [PATCH 5/5] Updated CHANGELOG.md, setup.py and __main__.py for the new release --- CHANGELOG.md | 22 +--------------------- bu_isciii/__main__.py | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 23 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a0fd384b..97ead2a86 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [2.2.4dev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.4 +## [2.2.4] - 2024-12-27 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.4 ### Credits @@ -27,26 +27,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Requirements -## [2.X.Xhot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.3 - -### Credits - -Code contributions to the hotfix: - -### Template fixes and updates - -### Modules - -#### Added enhancements - -#### Fixes - -#### Changed - -#### Removed - -### Requirements - ## [2.2.3] - 2024-12-23 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.3 ### Credits diff --git a/bu_isciii/__main__.py b/bu_isciii/__main__.py index 283f797c7..f06da05e5 100755 --- a/bu_isciii/__main__.py +++ b/bu_isciii/__main__.py @@ -57,7 +57,7 @@ def run_bu_isciii(): ) # stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = "2.2.3" + __version__ = "2.2.4" stderr.print( "[grey39] BU-ISCIII-tools version {}".format(__version__), highlight=False ) diff --git a/setup.py b/setup.py index 5e35992b5..483ba2e5c 100755 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "2.2.3" +version = "2.2.4" with open("README.md") as f: readme = f.read()