diff --git a/tasks/bioinfo_utils.wdl b/tasks/bioinfo_utils.wdl index 6241ccf..e128f4b 100644 --- a/tasks/bioinfo_utils.wdl +++ b/tasks/bioinfo_utils.wdl @@ -52,7 +52,7 @@ task indexVcf { cpu: 1 memory: in_index_mem + " GB" disks: "local-disk " + in_index_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } @@ -78,7 +78,7 @@ task fixVCFContigNaming { preemptible: 2 memory: in_index_mem + " GB" disks: "local-disk " + in_index_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } @@ -101,7 +101,7 @@ task removeHomRefs { preemptible: 2 memory: in_index_mem + " GB" disks: "local-disk " + in_index_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } @@ -175,7 +175,7 @@ task concatClippedVCFChunks { memory: mem_gb + " GB" cpu: 1 disks: "local-disk " + disk_size + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } diff --git a/workflows/giraffe.wdl b/workflows/giraffe.wdl index 8aad6a4..ed3e826 100644 --- a/workflows/giraffe.wdl +++ b/workflows/giraffe.wdl @@ -234,7 +234,8 @@ workflow Giraffe { in_merged_bam_file=mergeAlignmentBAMChunks.merged_bam_file, in_merged_bam_file_index=mergeAlignmentBAMChunks.merged_bam_file_index, in_path_list_file=pipeline_path_list_file, - in_prefix_to_strip=REFERENCE_PREFIX + in_prefix_to_strip=REFERENCE_PREFIX, + mem_gb=if MAP_MEM < 20 then MAP_MEM else 20 } ## diff --git a/workflows/giraffe_and_deeptrio.mapper.wdl b/workflows/giraffe_and_deeptrio.mapper.wdl index 36dc2e6..390d4fd 100644 --- a/workflows/giraffe_and_deeptrio.mapper.wdl +++ b/workflows/giraffe_and_deeptrio.mapper.wdl @@ -1042,7 +1042,7 @@ task concatClippedVCFChunks { time: 60 memory: in_call_mem + " GB" disks: "local-disk " + in_call_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } diff --git a/workflows/giraffe_and_deeptrio.wdl b/workflows/giraffe_and_deeptrio.wdl index ac3501d..740b273 100644 --- a/workflows/giraffe_and_deeptrio.wdl +++ b/workflows/giraffe_and_deeptrio.wdl @@ -1291,7 +1291,7 @@ task concatClippedVCFChunks { time: 60 memory: in_call_mem + " GB" disks: "local-disk " + in_call_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } diff --git a/workflows/giraffe_and_deepvariant.wdl b/workflows/giraffe_and_deepvariant.wdl index 1dacc29..a66b8bd 100644 --- a/workflows/giraffe_and_deepvariant.wdl +++ b/workflows/giraffe_and_deepvariant.wdl @@ -261,7 +261,8 @@ workflow GiraffeDeepVariant { in_merged_bam_file=mergeAlignmentBAMChunks.merged_bam_file, in_merged_bam_file_index=mergeAlignmentBAMChunks.merged_bam_file_index, in_path_list_file=pipeline_path_list_file, - in_prefix_to_strip=REFERENCE_PREFIX + in_prefix_to_strip=REFERENCE_PREFIX, + mem_gb=if MAP_MEM < 20 then MAP_MEM else 20 } ## diff --git a/workflows/giraffe_and_deepvariant_fromGAF.wdl b/workflows/giraffe_and_deepvariant_fromGAF.wdl index 0541f93..00d0c1f 100644 --- a/workflows/giraffe_and_deepvariant_fromGAF.wdl +++ b/workflows/giraffe_and_deepvariant_fromGAF.wdl @@ -139,7 +139,8 @@ workflow GiraffeDeepVariantFromGAF { in_merged_bam_file=sortBAM.sorted_bam, in_merged_bam_file_index=sortBAM.sorted_bam_index, in_path_list_file=pipeline_path_list_file, - in_prefix_to_strip=REFERENCE_PREFIX + in_prefix_to_strip=REFERENCE_PREFIX, + mem_gb=if VG_MEM < 20 then VG_MEM else 20 } ## diff --git a/workflows/vg_deeptrio_calling_workflow.wdl b/workflows/vg_deeptrio_calling_workflow.wdl index ace8f2d..73a1cb3 100644 --- a/workflows/vg_deeptrio_calling_workflow.wdl +++ b/workflows/vg_deeptrio_calling_workflow.wdl @@ -869,7 +869,7 @@ task concatClippedVCFChunks { time: 60 memory: in_mem + " GB" disks: "local-disk " + in_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } diff --git a/workflows/vg_indel_realign.wdl b/workflows/vg_indel_realign.wdl index b83cb84..28a7e40 100644 --- a/workflows/vg_indel_realign.wdl +++ b/workflows/vg_indel_realign.wdl @@ -41,7 +41,8 @@ workflow vgMultiMapCall { in_sample_name=SAMPLE_NAME, in_merged_bam_file=INPUT_BAM_FILE, in_merged_bam_file_index=INPUT_BAM_FILE_INDEX, - in_path_list_file=pipeline_path_list_file + in_path_list_file=pipeline_path_list_file, + mem_gb=if MAP_MEM < 20 then MAP_MEM else 20 } # Run distributed Indel Realignment on contig BAMs scatter (gatk_caller_input_files in splitBAMbyPath.bams_and_indexes_by_contig) { diff --git a/workflows/vg_multi_map_call.wdl b/workflows/vg_multi_map_call.wdl index 6b8fb84..45c5313 100644 --- a/workflows/vg_multi_map_call.wdl +++ b/workflows/vg_multi_map_call.wdl @@ -1429,7 +1429,7 @@ task runVCFClipper { runtime { memory: in_vgcall_mem + " GB" disks: "local-disk " + in_vgcall_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } @@ -1465,7 +1465,7 @@ task concatClippedVCFChunks { time: 60 memory: in_vgcall_mem + " GB" disks: "local-disk " + in_vgcall_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } @@ -1537,7 +1537,7 @@ task normalizeVCF { cpu: in_vgcall_cores memory: in_vgcall_mem + " GB" disks: "local-disk " + in_vgcall_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } diff --git a/workflows/vg_trio_giraffe_deeptrio_workflow.wdl b/workflows/vg_trio_giraffe_deeptrio_workflow.wdl index 5ddefd9..35901a2 100644 --- a/workflows/vg_trio_giraffe_deeptrio_workflow.wdl +++ b/workflows/vg_trio_giraffe_deeptrio_workflow.wdl @@ -531,7 +531,7 @@ task runSplitJointGenotypedVCF { cpu: in_cores memory: in_mem + " GB" disks: "local-disk " + in_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } @@ -782,7 +782,7 @@ task concatClippedVCFChunks { time: 60 memory: in_vgcall_mem + " GB" disks: "local-disk " + in_vgcall_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } @@ -860,7 +860,7 @@ task normalizeVCF { cpu: in_vgcall_cores memory: in_vgcall_mem + " GB" disks: "local-disk " + in_vgcall_disk + " SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } } diff --git a/workflows/vg_trio_multi_map_call.wdl b/workflows/vg_trio_multi_map_call.wdl index ad1fd36..d635ff0 100644 --- a/workflows/vg_trio_multi_map_call.wdl +++ b/workflows/vg_trio_multi_map_call.wdl @@ -610,7 +610,7 @@ task runSplitJointGenotypedVCF { runtime { memory: 50 + " GB" disks: "local-disk 100 SSD" - docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b" + docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0" } }