From c3ea13b964f12e820075e02e41fce0114df3aaea Mon Sep 17 00:00:00 2001 From: rernst Date: Thu, 15 Dec 2022 10:35:52 +0100 Subject: [PATCH 1/7] Remove module load java --- run_nextflow_wgs.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/run_nextflow_wgs.sh b/run_nextflow_wgs.sh index 9c87897..53c3277 100755 --- a/run_nextflow_wgs.sh +++ b/run_nextflow_wgs.sh @@ -28,8 +28,6 @@ sbatch < Date: Thu, 15 Dec 2022 10:36:03 +0100 Subject: [PATCH 2/7] Fix python command --- WGS.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS.nf b/WGS.nf index a73a66e..c3b70bb 100644 --- a/WGS.nf +++ b/WGS.nf @@ -219,7 +219,7 @@ process GetStatsFromFlagstat { script: """ - python ${baseDir}/assets/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt + python2 ${baseDir}/assets/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt """ } From 81121c54e4cf32fb70fe488c1d74d27768056c19 Mon Sep 17 00:00:00 2001 From: Linda Walraven-van Oijen Date: Fri, 10 Feb 2023 13:30:01 +0100 Subject: [PATCH 3/7] Added chmod processed runfolder --- run_nextflow_wgs.sh | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/run_nextflow_wgs.sh b/run_nextflow_wgs.sh index 9c87897..7b77878 100755 --- a/run_nextflow_wgs.sh +++ b/run_nextflow_wgs.sh @@ -55,11 +55,18 @@ if [ \$? -eq 0 ]; then rm workflow.running touch workflow.done + echo "Change permissions" + chmod 775 -R $output + exit 0 else echo "Nextflow failed" rm workflow.running touch workflow.failed + + echo "Change permissions" + chmod 775 -R $output + exit 1 fi EOT From beb6b5eff1c1c08970fe1bc66a772e56581ce453 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Fri, 17 Mar 2023 11:38:27 +0100 Subject: [PATCH 4/7] Add Zenodo badge --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 803a596..cbd9f3b 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ -# DxNextflowWGS +# DxNextflowWGS [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4709755.svg)](https://doi.org/10.5281/zenodo.4709755) + Genome Diagnostics Nextflow WGS workflow ## Get Nextflow Modules @@ -33,4 +34,4 @@ cp /guix/path.gz.squashfs baf_nextflow.gz.squashfs unsquashfs baf_nextflow.gz.squashfs chmod -R 0775 squashfs-root singularity build baf_nextflow.sif squashfs-root -``` \ No newline at end of file +``` From 4c0685ea0de454dbb8ce01134f0d0ab89a52c52c Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Wed, 31 May 2023 20:56:47 +0200 Subject: [PATCH 5/7] Update config and modules --- NextflowModules | 2 +- WGS.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/NextflowModules b/NextflowModules index a2f6cc8..c4f7982 160000 --- a/NextflowModules +++ b/NextflowModules @@ -1 +1 @@ -Subproject commit a2f6cc8caa20c3ccc39539bb0bde1a3d2ccd3cb9 +Subproject commit c4f7982e97a15d609851ad4422f421907c5a3dae diff --git a/WGS.config b/WGS.config index 5689888..a673268 100644 --- a/WGS.config +++ b/WGS.config @@ -2,7 +2,7 @@ params { genome = '/hpc/diaggen/data/databases/ref_genomes/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fasta' dxtracks_path = '/hpc/diaggen/software/production/Dx_tracks' - gatk_path = '/hpc/local/CentOS7/cog_bioinf/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar' + gatk_path = '/hpc/diaggen/software/tools/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar' gatk_bqsr_options = '--knownSites /hpc/diaggen/data/databases/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf.gz --knownSites /hpc/diaggen/data/databases/GATK_resource_bundle/b37/dbsnp_137.b37.vcf.gz --knownSites /hpc/diaggen/data/databases/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz' gatk_bqsr_pr_options = '--static_quantized_quals 10 --static_quantized_quals 20 --static_quantized_quals 30' fingerprint_target = 'fingerprint/81SNP_design.vcf' From f175eec106ff67c75ba4cad7342874e4edb60c30 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Fri, 9 Jun 2023 09:51:44 +0200 Subject: [PATCH 6/7] Update NextflowModules to v0.7.1 --- NextflowModules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NextflowModules b/NextflowModules index c4f7982..7bf677e 160000 --- a/NextflowModules +++ b/NextflowModules @@ -1 +1 @@ -Subproject commit c4f7982e97a15d609851ad4422f421907c5a3dae +Subproject commit 7bf677e0adbd90fee835569f505efe374a822b6a From 240cc44d35e7b6a5ac4b1e0a70ea6187a3d92bb5 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 29 Jun 2023 11:20:37 +0200 Subject: [PATCH 7/7] Update WGS.config - Fix ControlFreec_11_5_MakeGraph label --- WGS.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS.config b/WGS.config index a673268..f9c0df8 100644 --- a/WGS.config +++ b/WGS.config @@ -155,7 +155,7 @@ process { } } - withLabel: ControlFreec_11_5_makeGraph { + withLabel: ControlFreec_11_5_MakeGraph { cpus = 4 memory = { 5.GB * task.attempt } time = { (1.s * cnv_file.size() / 140) * task.attempt }