From c82624d259d079b43f4d2e3fa2b83697fda27bfe Mon Sep 17 00:00:00 2001 From: 5im1z Date: Mon, 24 Mar 2025 13:38:12 +0000 Subject: [PATCH 01/12] publish branch --- .dockstore.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.dockstore.yml b/.dockstore.yml index 3dbacf07..2e7cba5a 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -363,3 +363,4 @@ workflows: filters: # All tags, no branches branches: - vep-sv + - manta-dynamic-disk-size From 9a6c363eff8657bb517eb6880731579063a42e95 Mon Sep 17 00:00:00 2001 From: 5im1z Date: Mon, 24 Mar 2025 13:41:27 +0000 Subject: [PATCH 02/12] wip --- WGS_pipeline/Manta_SomaticSV_v1_0.wdl | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl index 88ffc92e..9ab3d54c 100644 --- a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl +++ b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl @@ -18,12 +18,18 @@ task Manta { File major_contig_bed="gs://ccleparams/manta_major_contigs.bed.gz" File major_contig_bed_index="gs://ccleparams/manta_major_contigs.bed.gz.tbi" - Int? disk_size - Int? mem_size - Int? cpu_num - Int? preemptible_attempts + Int preemptible = 2 + Int max_retries = 0 + Int cpu = 8 + Float mem_per_job_gb = 0.4 + Int additional_disk_gb = 0 } + Float jobs_per_cpu = 1.3 + Int num_jobs = round(cpu * jobs_per_cpu) + Int mem_gb = ceil(num_jobs * mem_per_job_gb) + Int disk_space = ceil(size(bam, "GiB")) + 10 + additional_disk_gb + command { EXTENSION="bam" EXTENSION_INDEX="bai" @@ -83,10 +89,11 @@ task Manta { } runtime { docker: "${manta_docker}" - memory: select_first([mem_size, 100]) + " GB" - cpu: select_first([cpu_num, 32]) - disks: "local-disk " + select_first([disk_size, 200]) + " SSD" - preemptible: select_first([preemptible_attempts, 3]) + memory: "~{mem_gb} GiB" + cpu: cpu + disks: "local-disk ~{disk_space} SSD" + preemptible: preemptible + maxRetries: max_retries } output { File germline_sv_vcf = "${sample_name}.diploidSV.vcf.gz" From 0e9ec6724f02657a385409431b782d3d44e0d65e Mon Sep 17 00:00:00 2001 From: 5im1z Date: Mon, 24 Mar 2025 13:43:02 +0000 Subject: [PATCH 03/12] debug --- WGS_pipeline/Manta_SomaticSV_v1_0.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl index 9ab3d54c..2c8ac5d5 100644 --- a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl +++ b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl @@ -28,7 +28,7 @@ task Manta { Float jobs_per_cpu = 1.3 Int num_jobs = round(cpu * jobs_per_cpu) Int mem_gb = ceil(num_jobs * mem_per_job_gb) - Int disk_space = ceil(size(bam, "GiB")) + 10 + additional_disk_gb + Int disk_space = ceil(size(tumor_bam, "GiB")) + 10 + additional_disk_gb command { EXTENSION="bam" From 548ab0a12a9ecd2d2b0b847f24508f42c1d7ea55 Mon Sep 17 00:00:00 2001 From: 5im1z Date: Mon, 24 Mar 2025 13:52:00 +0000 Subject: [PATCH 04/12] params --- WGS_pipeline/Manta_SomaticSV_v1_0.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl index 2c8ac5d5..2cc4eccc 100644 --- a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl +++ b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl @@ -67,8 +67,8 @@ task Manta { $major_contig_line ./runWorkflow.py --mode local \ - --jobs ${default=32 cpu_num} \ - --memGb ${default=100 mem_size} + --jobs ${default=32 cpu} \ + --memGb ${(${num_jobs} * 2)} # change the default names with sample prefix if [[ -f "${normal_bam}" ]]; then From 3364545b18e2c7a34bfe7ccae12f2a5651899012 Mon Sep 17 00:00:00 2001 From: 5im1z Date: Mon, 24 Mar 2025 13:56:27 +0000 Subject: [PATCH 05/12] syntax? --- WGS_pipeline/Manta_SomaticSV_v1_0.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl index 2cc4eccc..734d504f 100644 --- a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl +++ b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl @@ -68,7 +68,7 @@ task Manta { ./runWorkflow.py --mode local \ --jobs ${default=32 cpu} \ - --memGb ${(${num_jobs} * 2)} + --memGb $((~{num_jobs} * 2)) # change the default names with sample prefix if [[ -f "${normal_bam}" ]]; then From 7fde78dd8ae667641beaa177a15faf39c4a37fe2 Mon Sep 17 00:00:00 2001 From: 5im1z Date: Mon, 24 Mar 2025 14:03:07 +0000 Subject: [PATCH 06/12] additional disk --- WGS_pipeline/Manta_SomaticSV_v1_0.wdl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl index 734d504f..d9734b9f 100644 --- a/WGS_pipeline/Manta_SomaticSV_v1_0.wdl +++ b/WGS_pipeline/Manta_SomaticSV_v1_0.wdl @@ -155,6 +155,8 @@ workflow MantaSomaticSV { Boolean is_exome = defined(interval_list) Boolean is_cram Boolean is_major_contigs_only + + Int additional_disk_gb = 0 } if (is_exome) { @@ -176,7 +178,8 @@ workflow MantaSomaticSV { manta_docker = manta_docker, config_manta = config_manta, is_cram = is_cram, - is_major_contigs_only = is_major_contigs_only + is_major_contigs_only = is_major_contigs_only, + additional_disk_gb = additional_disk_gb } output { File germline_sv_vcf = Manta.germline_sv_vcf From 18e01910d280d2313a63bf48804974e8cc8d6de4 Mon Sep 17 00:00:00 2001 From: 5im1z Date: Mon, 24 Mar 2025 14:39:53 +0000 Subject: [PATCH 07/12] new wgs pipeline branch --- .dockstore.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.dockstore.yml b/.dockstore.yml index 2e7cba5a..e35a5b15 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -44,6 +44,7 @@ workflows: - master - guidemat-wdl - wgs-pipeline-no-cn + - manta-dynamic-disk-size - name: WGS_aggregate subclass: WDL publish: True From 7cd5e7bd21776b85c1b0b3b1e7964785c8dbf3b1 Mon Sep 17 00:00:00 2001 From: Simone Zhang Date: Mon, 16 Jun 2025 09:41:48 -0400 Subject: [PATCH 08/12] boot disc size is int --- WGS_pipeline/bcftools.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS_pipeline/bcftools.wdl b/WGS_pipeline/bcftools.wdl index 86f963ed..026fce8f 100644 --- a/WGS_pipeline/bcftools.wdl +++ b/WGS_pipeline/bcftools.wdl @@ -53,7 +53,7 @@ task bcftools_fix_ploidy { runtime { docker: docker - bootDiskSizeGb: "${boot_disk_size}" + bootDiskSizeGb: boot_disk_size memory: "${memory}GB" disks: "local-disk ${disk_space} SSD" cpu: "${num_threads}" From 666db80e3018c956d62d3663be33e79e3ec9e4c8 Mon Sep 17 00:00:00 2001 From: Simone Zhang Date: Mon, 16 Jun 2025 10:23:01 -0400 Subject: [PATCH 09/12] boot_disk_size is int --- WGS_pipeline/fix_mutect2.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS_pipeline/fix_mutect2.wdl b/WGS_pipeline/fix_mutect2.wdl index 61acccc3..60b088d6 100644 --- a/WGS_pipeline/fix_mutect2.wdl +++ b/WGS_pipeline/fix_mutect2.wdl @@ -59,7 +59,7 @@ task fix_mutect2 { runtime { docker: docker - bootDiskSizeGb: "${boot_disk_size}" + bootDiskSizeGb: boot_disk_size memory: "${memory} GB" disks: "local-disk ${disk_space} SSD" cpu: "${num_threads}" From 0f370eba173bcd365e9bf1e71f9c4e53f60f7221 Mon Sep 17 00:00:00 2001 From: Simone Zhang Date: Mon, 16 Jun 2025 10:23:35 -0400 Subject: [PATCH 10/12] boot_disk_size is int --- WGS_pipeline/mask_variants.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS_pipeline/mask_variants.wdl b/WGS_pipeline/mask_variants.wdl index 2422b40e..bfc04ca7 100644 --- a/WGS_pipeline/mask_variants.wdl +++ b/WGS_pipeline/mask_variants.wdl @@ -54,7 +54,7 @@ task bcftools_annotate { runtime { docker: docker - bootDiskSizeGb: "${boot_disk_size}" + bootDiskSizeGb: boot_disk_size memory: "${memory}GB" disks: "local-disk ${disk_space} SSD" cpu: "${num_threads}" From 85a7139a6f6b6bdd43ce61430a0684970f4cf31a Mon Sep 17 00:00:00 2001 From: Simone Zhang Date: Mon, 16 Jun 2025 10:24:14 -0400 Subject: [PATCH 11/12] boot_disk_size is int --- WGS_pipeline/opencravat.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS_pipeline/opencravat.wdl b/WGS_pipeline/opencravat.wdl index 2cbf32b1..2ecf1879 100644 --- a/WGS_pipeline/opencravat.wdl +++ b/WGS_pipeline/opencravat.wdl @@ -93,7 +93,7 @@ with open(sys.argv[1],'rb') as f: runtime { docker: docker - bootDiskSizeGb: "${boot_disk_size}" + bootDiskSizeGb: boot_disk_size memory: "${memory} GB" disks: "local-disk ${disk_space} SSD" cpu: "${num_threads}" From 443d22ead64d9f40c07af8a51ed519e9d1391c9e Mon Sep 17 00:00:00 2001 From: Simone Zhang Date: Mon, 16 Jun 2025 10:26:07 -0400 Subject: [PATCH 12/12] boot_disk_size is int --- WGS_pipeline/opencravat_dm.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WGS_pipeline/opencravat_dm.wdl b/WGS_pipeline/opencravat_dm.wdl index bb45e44c..0c4c8b46 100644 --- a/WGS_pipeline/opencravat_dm.wdl +++ b/WGS_pipeline/opencravat_dm.wdl @@ -122,7 +122,7 @@ with open(sys.argv[1],'rb') as f: runtime { docker: docker - bootDiskSizeGb: "${boot_disk_size}" + bootDiskSizeGb: boot_disk_size memory: "${memory} GB" disks: "local-disk ${disk_space} SSD" cpu: "${num_threads}"