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Allow testing Giraffe in small memory #143

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Allow testing Giraffe in small memory
adamnovak Jul 20, 2023
744f6a5
Depend on bcftools by a tag instead of a removed manifest's hash
adamnovak Jul 5, 2024
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8 changes: 4 additions & 4 deletions tasks/bioinfo_utils.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
}
}

Expand All @@ -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"
}
}

Expand All @@ -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"
}
}

Expand Down Expand Up @@ -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"
}
}

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3 changes: 2 additions & 1 deletion workflows/giraffe.wdl
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Expand Up @@ -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
}

##
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2 changes: 1 addition & 1 deletion workflows/giraffe_and_deeptrio.mapper.wdl
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Expand Up @@ -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"
}
}

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2 changes: 1 addition & 1 deletion workflows/giraffe_and_deeptrio.wdl
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Expand Up @@ -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"
}
}

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3 changes: 2 additions & 1 deletion workflows/giraffe_and_deepvariant.wdl
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Expand Up @@ -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
}

##
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3 changes: 2 additions & 1 deletion workflows/giraffe_and_deepvariant_fromGAF.wdl
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Expand Up @@ -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
}

##
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2 changes: 1 addition & 1 deletion workflows/vg_deeptrio_calling_workflow.wdl
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Expand Up @@ -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"
}
}

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3 changes: 2 additions & 1 deletion workflows/vg_indel_realign.wdl
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Expand Up @@ -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) {
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6 changes: 3 additions & 3 deletions workflows/vg_multi_map_call.wdl
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Expand Up @@ -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"
}
}

Expand Down Expand Up @@ -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"
}
}

Expand Down Expand Up @@ -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"
}
}

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6 changes: 3 additions & 3 deletions workflows/vg_trio_giraffe_deeptrio_workflow.wdl
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Expand Up @@ -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"
}
}

Expand Down Expand Up @@ -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"
}
}

Expand Down Expand Up @@ -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"
}
}

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2 changes: 1 addition & 1 deletion workflows/vg_trio_multi_map_call.wdl
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Expand Up @@ -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"
}
}

Expand Down