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🔨 Feature add skip norm flag #20

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Nov 21, 2024
Merged

🔨 Feature add skip norm flag #20

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5eb8cff
:hammer: added disable norm switch and modded tool requirements to fo…
migbro Nov 19, 2024
f8e545d
:pencil: update docs and bump version
migbro Nov 19, 2024
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5 changes: 5 additions & 0 deletions docs/SOMATIC_SNV_ANNOT_README.md
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Expand Up @@ -58,21 +58,26 @@ For each input, the sub-bullet refers to when to use the suggested input
- Mutect2: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MBQ,TLOD,HotSpotAllele"
- Lancet: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MS,FETS,HotSpotAllele"
- Vardict: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MSI,MSILEN,SOR,SSF,HotSpotAllele"
- Consensus: "gnomad_3_1_1_AC,gnomad_3_1_1_AN,gnomad_3_1_1_AF,gnomad_3_1_1_nhomalt,gnomad_3_1_1_AC_popmax,gnomad_3_1_1_AN_popmax,gnomad_3_1_1_AF_popmax,gnomad_3_1_1_nhomalt_popmax,gnomad_3_1_1_AC_controls_and_biobanks,gnomad_3_1_1_AN_controls_and_biobanks,gnomad_3_1_1_AF_controls_and_biobanks,gnomad_3_1_1_AF_non_cancer,gnomad_3_1_1_primate_ai_score,gnomad_3_1_1_splice_ai_consequence,gnomad_3_1_1_AF_non_cancer_afr,gnomad_3_1_1_AF_non_cancer_ami,gnomad_3_1_1_AF_non_cancer_asj,gnomad_3_1_1_AF_non_cancer_eas,gnomad_3_1_1_AF_non_cancer_fin,gnomad_3_1_1_AF_non_cancer_mid,gnomad_3_1_1_AF_non_cancer_nfe,gnomad_3_1_1_AF_non_cancer_oth,gnomad_3_1_1_AF_non_cancer_raw,gnomad_3_1_1_AF_non_cancer_sas,gnomad_3_1_1_AF_non_cancer_amr,gnomad_3_1_1_AF_non_cancer_popmax,gnomad_3_1_1_AF_non_cancer_all_popmax,gnomad_3_1_1_FILTER,MQ,MQ0,CAL,HotSpotAllele"
- `retain_ann` # Similar to above, if run for KF harmonization, recommend the following:
- Strelka2: "HGVSg"
- Mutect2: "HGVSg"
- Lancet: "HGVSg"
- Vardict: "HGVSg"
- Consensus: "HGVSg"
- `bcftools_strip_columns` # if reannotating an old file:
- "FILTER/GNOMAD_AF_HIGH,FILTER/NORM_DP_LOW,INFO/CSQ,INFO/HotSpotAllele" # recommended if re-annotating from an older VEP cache
- "FILTER/GNOMAD_AF_HIGH,FILTER/NORM_DP_LOW,INFO/HotSpotAllele" # recommended if repeating hot spot and want to keep VEP
- `bcftools_prefilter_csv` # if annotating a file with calls you want screen for, use this. i.e `FILTER="PASS"`
- `disable_norm` # set to `True` if existing input already normalized or of you have justification for skipping this step
- `disable_vep_annotation` # set to `True` if existing VEP annotation of file is ok
- `disable_hotspot_annotation` # set to `True` if existing HotSpot annotation is ok
- `tool_name`:
- `Strelka2`: `strelka2_somatic`
- `Mutect2`: `mutect2_somatic`
- `Lancet`: `lancet_somatic`
- `VarDict Java`: `vardict_somatic`
- `consensus`: `consensus_somatic`
- `vep_cores`: `16`
- `vep_ram`: `32`
- `vep_buffer`: `5000`
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4 changes: 2 additions & 2 deletions tools/add_strelka2_fields.cwl
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Expand Up @@ -46,10 +46,10 @@ inputs:
prefix: '--output_basename'
cores:
type: int?
default: 4
default: 8
ram:
type: int?
default: 3
default: 16
doc: 'RAM requirement in GB'

outputs:
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6 changes: 3 additions & 3 deletions tools/bcftools_strip_ann.cwl
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Expand Up @@ -6,8 +6,8 @@ requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: ResourceRequirement
ramMin: 8000
coresMin: 4
ramMin: 16000
coresMin: 8
- class: DockerRequirement
dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/vcfutils:latest'

Expand All @@ -18,7 +18,7 @@ arguments:
valueFrom: >-
set -eo pipefail

(bcftools annotate -x $(inputs.strip_info) $(inputs.input_vcf.path) -O z
(bcftools annotate -x $(inputs.strip_info) $(inputs.input_vcf.path) --threads 8 -O z
-o $(inputs.output_basename).$(inputs.tool_name).INFO_stripped.vcf.gz &&
tabix $(inputs.output_basename).$(inputs.tool_name).INFO_stripped.vcf.gz) ||
(echo "Check errors, likely does not have INFO, trying to pass input instead" >&2; cp $(inputs.input_vcf.path) .;
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4 changes: 2 additions & 2 deletions tools/gatk_variant_filter.cwl
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Expand Up @@ -6,8 +6,8 @@ requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: ResourceRequirement
ramMin: 8000
coresMin: 4
ramMin: 16000
coresMin: 8
- class: DockerRequirement
dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/gatk:4.1.1.0'

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4 changes: 2 additions & 2 deletions tools/generic_rename_outputs.cwl
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Expand Up @@ -6,8 +6,8 @@ requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: ResourceRequirement
ramMin: 2000
coresMin: 1
ramMin: 16000
coresMin: 8

baseCommand: []
arguments:
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4 changes: 2 additions & 2 deletions tools/hotspots_annotation.cwl
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Expand Up @@ -49,7 +49,7 @@ inputs:
csq_class: { type: 'string?', inputBinding: { position: 2, prefix: "--csq_class" }, doc: "Overrides the name of the CSQ field that stores variant class information" }

# Resource Control
ram: { type: 'int?', default: 2, doc: "GB of RAM to allocate to this task." }
cores: { type: 'int?', default: 1, doc: "CPU cores to allocate to this task." }
ram: { type: 'int?', default: 16, doc: "GB of RAM to allocate to this task." }
cores: { type: 'int?', default: 8, doc: "CPU cores to allocate to this task." }
outputs:
hotspots_vcf: { type: 'File', outputBinding: { glob: '*.gz', outputEval: '$(inputs.disable_hotspot_annotation ? inputs.input_vcf : self)' }, secondaryFiles: [.tbi] }
4 changes: 2 additions & 2 deletions tools/kf_mskcc_vcf2maf.cwl
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Expand Up @@ -5,8 +5,8 @@ requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: ResourceRequirement
ramMin: 4000
coresMin: 2
ramMin: 16000
coresMin: 8
- class: DockerRequirement
dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/kf_vcf2maf:v1.0.3'
- class: InitialWorkDirRequirement
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4 changes: 2 additions & 2 deletions tools/normalize_vcf.cwl
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Expand Up @@ -6,8 +6,8 @@ requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: ResourceRequirement
ramMin: 8000
coresMin: 4
ramMin: 16000
coresMin: 8
- class: DockerRequirement
dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/vcfutils:latest'

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