From 0ceed17519b2232c2d8639d4680a60f0c1f045c9 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 20 Sep 2023 13:38:06 -0700 Subject: [PATCH 1/5] reverse accidental ucla_cds false setting --- config/default.config | 2 +- external/pipeline-Nextflow-config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/default.config b/config/default.config index 1489631f..4e05233d 100644 --- a/config/default.config +++ b/config/default.config @@ -2,7 +2,7 @@ import nextflow.util.SysHelper params { //algorithm running environment - ucla_cds = false + ucla_cds = true cache_intermediate_pipeline_steps = false diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config index 5e51ab58..33d311dc 160000 --- a/external/pipeline-Nextflow-config +++ b/external/pipeline-Nextflow-config @@ -1 +1 @@ -Subproject commit 5e51ab584994f661639210cdb3a8c9817b944e53 +Subproject commit 33d311dc1e21b2284c1ec95fe1ef59f33fd9dd62 From 2635b1c47eb5f2284e049ba4602c99a7e98ab3a0 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 20 Sep 2023 14:33:44 -0700 Subject: [PATCH 2/5] pass readcount through filter process --- module/somaticsniper-processes.nf | 2 ++ module/somaticsniper.nf | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/module/somaticsniper-processes.nf b/module/somaticsniper-processes.nf index f7b6f5b1..d92fd8c1 100644 --- a/module/somaticsniper-processes.nf +++ b/module/somaticsniper-processes.nf @@ -236,6 +236,7 @@ process generate_ReadCount_bam_readcount { } // Run the false positive filter +// Output includes readcount file so compression can be delayed until after this process process filter_FalsePositive_SomaticSniper { container params.docker_image_somaticsniper publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}", @@ -254,6 +255,7 @@ process filter_FalsePositive_SomaticSniper { output: path "*.SNPfilter.fp_pass", emit: fp_pass path "*.SNPfilter.fp_fail", emit: fp_fail + path readcount_file, emit: readcount path ".command.*" """ diff --git a/module/somaticsniper.nf b/module/somaticsniper.nf index 1fa95f31..587ba468 100644 --- a/module/somaticsniper.nf +++ b/module/somaticsniper.nf @@ -55,7 +55,7 @@ workflow somaticsniper { generate_ReadCount_bam_readcount(params.reference,create_ReadCountPosition_SomaticSniper.out.snp_positions, tumor_bam, tumor_index) filter_FalsePositive_SomaticSniper(apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor, generate_ReadCount_bam_readcount.out.readcount) call_HighConfidenceSNV_SomaticSniper(filter_FalsePositive_SomaticSniper.out.fp_pass) - compress_file_blarchive(generate_ReadCount_bam_readcount.out.readcount + compress_file_blarchive(filter_FalsePositive_SomaticSniper.out.readcount .map{ it -> ['readcount', it] }) // rename_samples_BCFtools needs bgzipped input compress_index_VCF_hc(call_HighConfidenceSNV_SomaticSniper.out.hc From 86da0806d10d2673891acd95749ac378145d7811 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Wed, 20 Sep 2023 14:47:35 -0700 Subject: [PATCH 3/5] update changelog --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 13c992af..b003600e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +### Changed +- Fix readcount compression: delayed + ## [7.0.0-rc.1] - 2023-08-28 ### Added From e5cd9e330d433e81c7099f9b144fc84a73eb7e5a Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 21 Sep 2023 17:29:06 -0700 Subject: [PATCH 4/5] update to avoid readcount pass-through --- module/somaticsniper-processes.nf | 2 -- module/somaticsniper.nf | 8 ++++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/module/somaticsniper-processes.nf b/module/somaticsniper-processes.nf index d92fd8c1..f7b6f5b1 100644 --- a/module/somaticsniper-processes.nf +++ b/module/somaticsniper-processes.nf @@ -236,7 +236,6 @@ process generate_ReadCount_bam_readcount { } // Run the false positive filter -// Output includes readcount file so compression can be delayed until after this process process filter_FalsePositive_SomaticSniper { container params.docker_image_somaticsniper publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}", @@ -255,7 +254,6 @@ process filter_FalsePositive_SomaticSniper { output: path "*.SNPfilter.fp_pass", emit: fp_pass path "*.SNPfilter.fp_fail", emit: fp_fail - path readcount_file, emit: readcount path ".command.*" """ diff --git a/module/somaticsniper.nf b/module/somaticsniper.nf index 587ba468..e6a34f5f 100644 --- a/module/somaticsniper.nf +++ b/module/somaticsniper.nf @@ -55,8 +55,12 @@ workflow somaticsniper { generate_ReadCount_bam_readcount(params.reference,create_ReadCountPosition_SomaticSniper.out.snp_positions, tumor_bam, tumor_index) filter_FalsePositive_SomaticSniper(apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor, generate_ReadCount_bam_readcount.out.readcount) call_HighConfidenceSNV_SomaticSniper(filter_FalsePositive_SomaticSniper.out.fp_pass) - compress_file_blarchive(filter_FalsePositive_SomaticSniper.out.readcount - .map{ it -> ['readcount', it] }) + // combining to delay compression until after filtering step + compress_file_blarchive( + generate_ReadCount_bam_readcount.out.readcount + .combine(filter_FalsePositive_SomaticSniper.out.fp_pass.collect()) + .map{ it -> ['readcount', it[0]] } + ) // rename_samples_BCFtools needs bgzipped input compress_index_VCF_hc(call_HighConfidenceSNV_SomaticSniper.out.hc .map{ it -> ['SNV', it] }) From 78197954ab2395084ec73283933764b6fdffe36c Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon <3223552+sorelfitzgibbon@users.noreply.github.com> Date: Fri, 22 Sep 2023 08:53:50 -0700 Subject: [PATCH 5/5] Update CHANGELOG.md Co-authored-by: Yash Patel <86321070+yashpatel6@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b003600e..32347152 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Changed -- Fix readcount compression: delayed +- Delay readcount compression until original file is no longer needed ## [7.0.0-rc.1] - 2023-08-28