From af67af8875704828dce90250d94aafd39fd78770 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 14 Dec 2023 10:26:30 -0600 Subject: [PATCH 01/17] adding somatic wgs to dockstore --- .dockstore.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.dockstore.yml b/.dockstore.yml index 8e313cc4..8576cbb4 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -1,8 +1,8 @@ version: 1.2 workflows: - subclass: WDL - primaryDescriptorPath: /definitions/immuno.wdl - name: immuno + primaryDescriptorPath: /definitions/soamtic_wgs.wdl + name: somatic_wgs authors: - orcid: 0000-0003-4266-6700 #chrisamiller - orcid: 0000-0002-6388-446X #malachig From 0b3ab557dddb1baee77d2cc1c398921a63f96d49 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 14 Dec 2023 10:35:12 -0600 Subject: [PATCH 02/17] last typo fix in year 2023 --- .dockstore.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.dockstore.yml b/.dockstore.yml index 8576cbb4..0bf0cd9f 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -1,7 +1,7 @@ version: 1.2 workflows: - subclass: WDL - primaryDescriptorPath: /definitions/soamtic_wgs.wdl + primaryDescriptorPath: /definitions/somatic_wgs.wdl name: somatic_wgs authors: - orcid: 0000-0003-4266-6700 #chrisamiller From e227bc79abf30f596ba7ec967101284162c4ed1c Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 14 Dec 2023 10:54:42 -0600 Subject: [PATCH 03/17] edit dockstore to reflect both workflows --- .dockstore.yml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/.dockstore.yml b/.dockstore.yml index 0bf0cd9f..a40eaa2b 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -1,5 +1,32 @@ version: 1.2 workflows: + - subclass: WDL + primaryDescriptorPath: /definitions/immuno.wdl + name: immuno + authors: + - orcid: 0000-0003-4266-6700 #chrisamiller + - orcid: 0000-0002-6388-446X #malachig + - orcid: 0000-0003-4378-7328 #susannasiebert + - orcid: 0000-0002-0577-4705 #tmooney + - orcid: 0000-0001-6293-4632 #sridhar0605 + - orcid: 0009-0002-2565-0774 #johnegarza + - orcid: 0000-0001-7547-5789 #jasonwalker80 + - orcid: 0000-0003-1928-7139 #zlskidmore + - orcid: 0000-0002-7648-1360 #bryanfisk + - orcid: 0000-0003-0944-3126 #acoffman + - orcid: 0000-0002-2584-5320 #jhundal + - orcid: 0000-0002-9704-408X #Matthew-Mosior + - orcid: 0000-0002-3024-6891 #apaul7 + - name: John Maruska #johnmaruska + - name: Layth Aljorani #Layth17 + - name: Sai Mukund Ramakrishnan #saimukund20 + - name: Feiyu Du #dufeiyu + - name: Saad Khan #smk5g5 + - name: Samuel Peters #sam16711 + - name: Agata Gruszczynska #GruA + - name: Gue Su Chang #guesu, gschang + - name: Irenaeus Chan #IrenaeusChan + - name: Chad Tomlinson #chad388 - subclass: WDL primaryDescriptorPath: /definitions/somatic_wgs.wdl name: somatic_wgs From c986c326ce00b640643537cafaa7195cf8eb04e8 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Fri, 15 Dec 2023 11:07:08 -0600 Subject: [PATCH 04/17] variant call wdl --- .dockstore.yml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/.dockstore.yml b/.dockstore.yml index a40eaa2b..7ed51ce5 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -54,3 +54,30 @@ workflows: - name: Gue Su Chang #guesu, gschang - name: Irenaeus Chan #IrenaeusChan - name: Chad Tomlinson #chad388 +- subclass: WDL + primaryDescriptorPath: /definitions/detect_variants_wgs.wdl + name: detect_variants_wgs + authors: + - orcid: 0000-0003-4266-6700 #chrisamiller + - orcid: 0000-0002-6388-446X #malachig + - orcid: 0000-0003-4378-7328 #susannasiebert + - orcid: 0000-0002-0577-4705 #tmooney + - orcid: 0000-0001-6293-4632 #sridhar0605 + - orcid: 0009-0002-2565-0774 #johnegarza + - orcid: 0000-0001-7547-5789 #jasonwalker80 + - orcid: 0000-0003-1928-7139 #zlskidmore + - orcid: 0000-0002-7648-1360 #bryanfisk + - orcid: 0000-0003-0944-3126 #acoffman + - orcid: 0000-0002-2584-5320 #jhundal + - orcid: 0000-0002-9704-408X #Matthew-Mosior + - orcid: 0000-0002-3024-6891 #apaul7 + - name: John Maruska #johnmaruska + - name: Layth Aljorani #Layth17 + - name: Sai Mukund Ramakrishnan #saimukund20 + - name: Feiyu Du #dufeiyu + - name: Saad Khan #smk5g5 + - name: Samuel Peters #sam16711 + - name: Agata Gruszczynska #GruA + - name: Gue Su Chang #guesu, gschang + - name: Irenaeus Chan #IrenaeusChan + - name: Chad Tomlinson #chad388 From d29b72990a0fcb9a6693192fdba8e2c696251fcb Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Fri, 15 Dec 2023 11:35:40 -0600 Subject: [PATCH 05/17] fix indent --- .dockstore.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.dockstore.yml b/.dockstore.yml index 7ed51ce5..910feb0a 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -54,7 +54,7 @@ workflows: - name: Gue Su Chang #guesu, gschang - name: Irenaeus Chan #IrenaeusChan - name: Chad Tomlinson #chad388 -- subclass: WDL + - subclass: WDL primaryDescriptorPath: /definitions/detect_variants_wgs.wdl name: detect_variants_wgs authors: From 6c5a89bdf1a22094f73b82e0bb32900b770a8f0f Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Wed, 17 Jan 2024 12:18:39 -0600 Subject: [PATCH 06/17] upgrading haplotype caller version and increasing mutect2 mem --- definitions/tools/docm_gatk_haplotype_caller.wdl | 2 +- definitions/tools/mutect.wdl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/definitions/tools/docm_gatk_haplotype_caller.wdl b/definitions/tools/docm_gatk_haplotype_caller.wdl index 16d9e0d2..d9e15642 100644 --- a/definitions/tools/docm_gatk_haplotype_caller.wdl +++ b/definitions/tools/docm_gatk_haplotype_caller.wdl @@ -27,7 +27,7 @@ task docmGatkHaplotypeCaller { preemptible: 1 maxRetries: 2 memory: "9GB" - docker: "broadinstitute/gatk:4.1.2.0" + docker: "broadinstitute/gatk:4.1.3.0" disks: "local-disk ~{space_needed_gb} HDD" } diff --git a/definitions/tools/mutect.wdl b/definitions/tools/mutect.wdl index a165b8f9..f7cf0fbb 100644 --- a/definitions/tools/mutect.wdl +++ b/definitions/tools/mutect.wdl @@ -29,7 +29,7 @@ task mutect { preemptible: 1 maxRetries: 2 docker: "broadinstitute/gatk:4.2.3.0" - memory: "2GB" + memory: "8GB" bootDiskSizeGb: space_needed_gb disks: "local-disk ~{space_needed_gb} HDD" } From 53507a96e4b6dddf1f15e34d1a44d12bfcdb116b Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 14:36:34 -0600 Subject: [PATCH 07/17] detect variant cram input --- definitions/detect_variants_wgs.wdl | 81 ++++++++++++------- .../subworkflows/cram_to_bam_and_index.wdl | 35 ++++++++ 2 files changed, 87 insertions(+), 29 deletions(-) create mode 100644 definitions/subworkflows/cram_to_bam_and_index.wdl diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index b73dba88..e67737f0 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -6,6 +6,7 @@ import "subworkflows/mutect.wdl" as m import "subworkflows/strelka_and_post_processing.wdl" as sapp import "subworkflows/varscan_pre_and_post_processing.wdl" as vpapp import "subworkflows/vcf_readcount_annotator.wdl" as vra +import "subworkflows/cram_to_bam_and_index.wdl" as cb import "tools/add_vep_fields_to_table.wdl" as avftt import "tools/bam_readcount.wdl" as br import "tools/bgzip.wdl" as b @@ -22,10 +23,10 @@ workflow detectVariantsWgs { File reference File reference_fai File reference_dict - File tumor_bam - File tumor_bam_bai - File normal_bam - File normal_bam_bai + File tumor_cram + File tumor_cram_bai + File normal_cram + File normal_cram_bai File roi_intervals Boolean strelka_exome_mode Int strelka_cpu_reserved = 8 @@ -54,13 +55,13 @@ workflow detectVariantsWgs { String gnomad_field_name = "gnomADe_AF" # only change with gnomad_filter_annotation Float filter_gnomADe_maximum_population_allele_frequency = 0.001 - Float filter_mapq0_threshold = 0.15 + Float filter_mapq0_threshold = 0.10 Int filter_minimum_depth = 1 Float? filter_somatic_llr_threshold Float? filter_somatic_llr_tumor_purity Float? filter_somatic_llr_normal_contamination_rate Boolean cle_vcf_filter = false - Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] + Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF","LLR"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"] String tumor_sample_name @@ -68,6 +69,27 @@ workflow detectVariantsWgs { Array[VepCustomAnnotation] vep_custom_annotations File? validated_variants File? validated_variants_tbi + String prefix # workflow final output prefix + } + + call cb.cramTobamAndIndex as tumorConvert { + input: + reference=reference, + reference_fai=reference_fai, + reference_dict=reference_dict, + cram=tumor_cram + cram_index=tumor_cram_index + + } + + call cb.cramTobamAndIndex as normalConvert { + input: + reference=reference, + reference_fai=reference_fai, + reference_dict=reference_dict, + cram=normal_cram + cram_index=normal_cram_index + } call m.mutect { @@ -75,10 +97,10 @@ workflow detectVariantsWgs { reference=reference, reference_fai=reference_fai, reference_dict=reference_dict, - tumor_bam=tumor_bam, - tumor_bam_bai=tumor_bam_bai, - normal_bam=normal_bam, - normal_bam_bai=normal_bam_bai, + tumor_bam=tumorConvert.indexed_bam, + tumor_bam_bai=tumorConvert.indexed_bam_bai, + normal_bam=normalConvert.indexed_bam, + normal_bam_bai=normalConvert.indexed_bam_bai, interval_list=roi_intervals, scatter_count=scatter_count, tumor_sample_name=tumor_sample_name, @@ -92,12 +114,12 @@ workflow detectVariantsWgs { reference_dict=reference_dict, tumor_sample_name=tumor_sample_name, - tumor_bam=tumor_bam, - tumor_bam_bai=tumor_bam_bai, + tumor_bam=tumorConvert.indexed_bam, + tumor_bam_bai=tumorConvert.indexed_bam_bai, normal_sample_name=normal_sample_name, - normal_bam=normal_bam, - normal_bam_bai=normal_bam_bai, + normal_bam=normalConvert.indexed_bam, + normal_bam_bai=normalConvert.indexed_bam_bai, interval_list=roi_intervals, exome_mode=strelka_exome_mode, @@ -114,12 +136,12 @@ workflow detectVariantsWgs { reference_dict=reference_dict, tumor_sample_name=tumor_sample_name, - tumor_bam=tumor_bam, - tumor_bam_bai=tumor_bam_bai, + tumor_bam=tumorConvert.indexed_bam, + tumor_bam_bai=tumorConvert.indexed_bam_bai, normal_sample_name=normal_sample_name, - normal_bam=normal_bam, - normal_bam_bai=normal_bam_bai, + normal_bam=normalConvert.indexed_bam, + normal_bam_bai=normalConvert.indexed_bam_bai, interval_list=roi_intervals, scatter_count=scatter_count, @@ -136,11 +158,11 @@ workflow detectVariantsWgs { reference_fai=reference_fai, reference_dict=reference_dict, - tumor_bam=tumor_bam, - tumor_bam_bai=tumor_bam_bai, + tumor_bam=tumorConvert.indexed_bam, + tumor_bam_bai=tumorConvert.indexed_bam_bai, - normal_bam=normal_bam, - normal_bam_bai=normal_bam_bai, + normal_bam=normalConvert.indexed_bam, + normal_bam_bai=normalConvert.indexed_bam_bai, interval_list=roi_intervals, docm_vcf=docm_vcf, @@ -207,8 +229,8 @@ workflow detectVariantsWgs { reference_fai=reference_fai, reference_dict=reference_dict, sample=tumor_sample_name, - bam=tumor_bam, - bam_bai=tumor_bam_bai, + bam=tumorConvert.indexed_bam, + bam_bai=tumorConvert.indexed_bam_bai, min_base_quality=readcount_minimum_base_quality, min_mapping_quality=readcount_minimum_mapping_quality } @@ -220,8 +242,8 @@ workflow detectVariantsWgs { reference_fai=reference_fai, reference_dict=reference_dict, sample=normal_sample_name, - bam=normal_bam, - bam_bai=normal_bam_bai, + bam=normalConvert.indexed_bam, + bam_bai=normalConvert.indexed_bam_bai, min_base_quality=readcount_minimum_base_quality, min_mapping_quality=readcount_minimum_mapping_quality } @@ -258,8 +280,8 @@ workflow detectVariantsWgs { filter_somatic_llr_tumor_purity=filter_somatic_llr_tumor_purity, filter_somatic_llr_normal_contamination_rate=filter_somatic_llr_normal_contamination_rate, filter_minimum_depth=filter_minimum_depth, - tumor_bam=tumor_bam, - tumor_bam_bai=tumor_bam_bai, + tumor_bam=tumorConvert.indexed_bam, + tumor_bam_bai=tumorConvert.indexed_bam_bai, do_cle_vcf_filter=cle_vcf_filter, reference=reference, reference_fai=reference_fai, @@ -294,7 +316,8 @@ workflow detectVariantsWgs { input: vcf=annotatedFilterIndex.indexed_vcf, tsv=variantsToTable.variants_tsv, - vep_fields=vep_to_table_fields + vep_fields=vep_to_table_fields, + prefix=prefix } output { diff --git a/definitions/subworkflows/cram_to_bam_and_index.wdl b/definitions/subworkflows/cram_to_bam_and_index.wdl new file mode 100644 index 00000000..c55e054a --- /dev/null +++ b/definitions/subworkflows/cram_to_bam_and_index.wdl @@ -0,0 +1,35 @@ +version 1.0 + +import "../tools/cram_to_bam.wdl" as cb +import "../tools/index_bam.wdl" as i + +workflow cramTobamAndIndex{ + input{ + File cram + File cram_index + File reference + File reference_index + File reference_dict + } + + call cb.cramToBam { + input: + cram=cram, + cram_index=cram_index, + reference=reference, + reference_fai=reference_fai, + reference_dict=reference_dict, + } + + call i.index_bam { + input: + bam=cramToBam.bam + } + + output { + File indexed_bam = index_bam.indexed_bam + File indexed_bam_bai = index_bam.indexed_bam_bai + File indexed_bai = index_bam.indexed_bai + + } +} \ No newline at end of file From c00f59e479a23b5d8819850fb5f52c8e7a882750 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 14:40:32 -0600 Subject: [PATCH 08/17] typo --- definitions/detect_variants_wgs.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index e67737f0..823ec052 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -24,9 +24,9 @@ workflow detectVariantsWgs { File reference_fai File reference_dict File tumor_cram - File tumor_cram_bai + File tumor_cram_index File normal_cram - File normal_cram_bai + File normal_cram_index File roi_intervals Boolean strelka_exome_mode Int strelka_cpu_reserved = 8 From 9e1503c2e6858189ebf340a9b092d2d403f9ceac Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 14:45:57 -0600 Subject: [PATCH 09/17] typos --- definitions/detect_variants_wgs.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index 823ec052..64969305 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -77,7 +77,7 @@ workflow detectVariantsWgs { reference=reference, reference_fai=reference_fai, reference_dict=reference_dict, - cram=tumor_cram + cram=tumor_cram, cram_index=tumor_cram_index } @@ -87,7 +87,7 @@ workflow detectVariantsWgs { reference=reference, reference_fai=reference_fai, reference_dict=reference_dict, - cram=normal_cram + cram=normal_cram, cram_index=normal_cram_index } From cae2a9b99967ff7e52a1dee08968ae9b5218bc4e Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 14:56:41 -0600 Subject: [PATCH 10/17] typos tools --- definitions/subworkflows/cram_to_bam_and_index.wdl | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/definitions/subworkflows/cram_to_bam_and_index.wdl b/definitions/subworkflows/cram_to_bam_and_index.wdl index c55e054a..cdc5088f 100644 --- a/definitions/subworkflows/cram_to_bam_and_index.wdl +++ b/definitions/subworkflows/cram_to_bam_and_index.wdl @@ -4,7 +4,7 @@ import "../tools/cram_to_bam.wdl" as cb import "../tools/index_bam.wdl" as i workflow cramTobamAndIndex{ - input{ + input { File cram File cram_index File reference @@ -18,7 +18,7 @@ workflow cramTobamAndIndex{ cram_index=cram_index, reference=reference, reference_fai=reference_fai, - reference_dict=reference_dict, + reference_dict=reference_dict } call i.index_bam { @@ -30,6 +30,5 @@ workflow cramTobamAndIndex{ File indexed_bam = index_bam.indexed_bam File indexed_bam_bai = index_bam.indexed_bam_bai File indexed_bai = index_bam.indexed_bai - } } \ No newline at end of file From c5a60f79254c8dddf2378e46a26d0578e5eebdfe Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 14:58:46 -0600 Subject: [PATCH 11/17] typos indexbam --- definitions/subworkflows/cram_to_bam_and_index.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/definitions/subworkflows/cram_to_bam_and_index.wdl b/definitions/subworkflows/cram_to_bam_and_index.wdl index cdc5088f..f35055dc 100644 --- a/definitions/subworkflows/cram_to_bam_and_index.wdl +++ b/definitions/subworkflows/cram_to_bam_and_index.wdl @@ -21,7 +21,7 @@ workflow cramTobamAndIndex{ reference_dict=reference_dict } - call i.index_bam { + call i.indexBam { input: bam=cramToBam.bam } From 94165ff5dab6ba9026d1876df4352c2ddb3a089f Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 15:02:08 -0600 Subject: [PATCH 12/17] indexBam typos --- definitions/subworkflows/cram_to_bam_and_index.wdl | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/definitions/subworkflows/cram_to_bam_and_index.wdl b/definitions/subworkflows/cram_to_bam_and_index.wdl index f35055dc..e8f36b31 100644 --- a/definitions/subworkflows/cram_to_bam_and_index.wdl +++ b/definitions/subworkflows/cram_to_bam_and_index.wdl @@ -17,18 +17,17 @@ workflow cramTobamAndIndex{ cram=cram, cram_index=cram_index, reference=reference, - reference_fai=reference_fai, + reference_fai=reference_index, reference_dict=reference_dict } call i.indexBam { - input: - bam=cramToBam.bam + input: bam=cramToBam.bam } output { - File indexed_bam = index_bam.indexed_bam - File indexed_bam_bai = index_bam.indexed_bam_bai - File indexed_bai = index_bam.indexed_bai + File indexed_bam = indexBam.indexed_bam + File indexed_bam_bai = indexBam.indexed_bam_bai + File indexed_bai = indexBam.indexed_bai } } \ No newline at end of file From bc27cf018811f9ee3b4f7ca8d701dabc1c99611f Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 15:04:20 -0600 Subject: [PATCH 13/17] indexBam typos1 --- definitions/subworkflows/cram_to_bam_and_index.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/definitions/subworkflows/cram_to_bam_and_index.wdl b/definitions/subworkflows/cram_to_bam_and_index.wdl index e8f36b31..0e341b82 100644 --- a/definitions/subworkflows/cram_to_bam_and_index.wdl +++ b/definitions/subworkflows/cram_to_bam_and_index.wdl @@ -17,7 +17,7 @@ workflow cramTobamAndIndex{ cram=cram, cram_index=cram_index, reference=reference, - reference_fai=reference_index, + reference_index=reference_index, reference_dict=reference_dict } From ff3949e482588d41cb94b457c317ce760200efa9 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 15:10:24 -0600 Subject: [PATCH 14/17] detect_variant typo --- definitions/detect_variants_wgs.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index 64969305..00055bb6 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -75,7 +75,7 @@ workflow detectVariantsWgs { call cb.cramTobamAndIndex as tumorConvert { input: reference=reference, - reference_fai=reference_fai, + reference_index=reference_fai, reference_dict=reference_dict, cram=tumor_cram, cram_index=tumor_cram_index @@ -85,7 +85,7 @@ workflow detectVariantsWgs { call cb.cramTobamAndIndex as normalConvert { input: reference=reference, - reference_fai=reference_fai, + reference_index=reference_fai, reference_dict=reference_dict, cram=normal_cram, cram_index=normal_cram_index From 026a7a7222bf48e6c7b2660e18bdfdb108b0396e Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 15:17:26 -0600 Subject: [PATCH 15/17] somatic wgs --- definitions/somatic_wgs.wdl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/definitions/somatic_wgs.wdl b/definitions/somatic_wgs.wdl index d68159fc..7d3a7cc5 100644 --- a/definitions/somatic_wgs.wdl +++ b/definitions/somatic_wgs.wdl @@ -177,10 +177,10 @@ workflow somaticWgs { reference=reference, reference_fai=reference_fai, reference_dict=reference_dict, - tumor_bam=tumorAlignment.final_bam, - tumor_bam_bai=tumorAlignment.final_bam_bai, - normal_bam=normalAlignment.final_bam, - normal_bam_bai=normalAlignment.final_bam_bai, + tumor_cram=tumorAlignment.final_bam, + tumor_cram_bai=tumorAlignment.final_bam_bai, + normal_cram=normalAlignment.final_bam, + normal_cram_bai=normalAlignment.final_bam_bai, roi_intervals=target_intervals, strelka_exome_mode=false, strelka_cpu_reserved=strelka_cpu_reserved, From 6638a353efecead0514d69d9b119da690d0fc2c1 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Thu, 25 Jan 2024 15:19:41 -0600 Subject: [PATCH 16/17] somatic wgs typi --- definitions/somatic_wgs.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/definitions/somatic_wgs.wdl b/definitions/somatic_wgs.wdl index 7d3a7cc5..9972c794 100644 --- a/definitions/somatic_wgs.wdl +++ b/definitions/somatic_wgs.wdl @@ -178,9 +178,9 @@ workflow somaticWgs { reference_fai=reference_fai, reference_dict=reference_dict, tumor_cram=tumorAlignment.final_bam, - tumor_cram_bai=tumorAlignment.final_bam_bai, + tumor_cram_index=tumorAlignment.final_bam_bai, normal_cram=normalAlignment.final_bam, - normal_cram_bai=normalAlignment.final_bam_bai, + normal_cram_index=normalAlignment.final_bam_bai, roi_intervals=target_intervals, strelka_exome_mode=false, strelka_cpu_reserved=strelka_cpu_reserved, From defc97083ea20960415f54b7e9063dd6952d7c99 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sat, 27 Jan 2024 08:25:11 -0600 Subject: [PATCH 17/17] increase cram to bam mem --- definitions/tools/cram_to_bam.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/definitions/tools/cram_to_bam.wdl b/definitions/tools/cram_to_bam.wdl index b4666fb6..3f1f6a4b 100644 --- a/definitions/tools/cram_to_bam.wdl +++ b/definitions/tools/cram_to_bam.wdl @@ -9,9 +9,9 @@ task cramToBam { File reference_dict } - Int space_needed_gb = 10 + round(size([cram, cram_index, reference, reference_index, reference_dict], "GB") * 3) + Int space_needed_gb = 10 + round(size([cram, cram_index, reference, reference_index, reference_dict], "GB") * 5) runtime { - memory: "4GB" + memory: "8GB" docker: "quay.io/biocontainers/samtools:1.11--h6270b1f_0" disks: "local-disk ~{space_needed_gb} HDD" }