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Add option to ignore masked reference #3

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Add option to ignore masked reference #3

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2 changes: 2 additions & 0 deletions clinical-validation.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ workflow ClinicalValidation {
File referenceFasta
File referenceFastaFai
File referenceFastaDict
Boolean ignoreMaskedRef = false
Array[ValidationUnit]+ validationUnit
File? highConfidenceIntervals
File? regions
Expand Down Expand Up @@ -68,6 +69,7 @@ workflow ClinicalValidation {
referenceFasta = referenceFasta,
referenceFastaFai = referenceFastaFai,
outputPath = unit.outputPrefix + "_baseline_normalizedCalls.vcf",
ignoreMaskedRef = ignoreMaskedRef,
dockerImage = dockerImages["vt"]
}

Expand Down
2 changes: 1 addition & 1 deletion tasks
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Submodule tasks updated 52 files
+1 −0 .github/PULL_REQUEST_TEMPLATE.md
+151 −17 CHANGELOG.md
+3 −0 CPAT.wdl
+1 −1 VERSION
+127 −0 bam2fastx.wdl
+270 −6 bcftools.wdl
+43 −37 bedtools.wdl
+1 −1 biopet/bamstats.wdl
+21 −59 biopet/biopet.wdl
+3 −3 biopet/sampleconfig.wdl
+1 −1 biopet/seqstat.wdl
+5 −0 biowdl.wdl
+4 −6 bowtie.wdl
+116 −0 bwa-mem2.wdl
+36 −77 bwa.wdl
+92 −0 ccs.wdl
+45 −33 centrifuge.wdl
+62 −8 chunked-scatter.wdl
+7 −1 clever.wdl
+15 −22 collect-columns.wdl
+10 −1 common.wdl
+75 −232 cutadapt.wdl
+4 −1 delly.wdl
+41 −23 fastqc.wdl
+284 −107 gatk.wdl
+4 −0 gffcompare.wdl
+3 −0 gffread.wdl
+84 −0 gridss.wdl
+33 −11 hisat2.wdl
+21 −49 htseq.wdl
+91 −0 isoseq3.wdl
+163 −0 lima.wdl
+6 −0 manta.wdl
+25 −19 minimap2.wdl
+45 −23 multiqc.wdl
+74 −0 pbmm2.wdl
+244 −97 picard.wdl
+10 −4 rtg.wdl
+151 −0 sambamba.wdl
+242 −137 samtools.wdl
+1 −1 scripts
+72 −0 smoove.wdl
+15 −0 somaticseq.wdl
+97 −5 star.wdl
+6 −0 strelka.wdl
+32 −93 stringtie.wdl
+3 −0 survivor.wdl
+238 −92 talon.wdl
+49 −41 transcriptclean.wdl
+16 −8 umi-tools.wdl
+5 −2 vardict.wdl
+10 −2 vt.wdl
14 changes: 14 additions & 0 deletions tests/integration/ignoreMaskedRef.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
{
"ClinicalValidation.referenceFasta": "tests/data/reference.fasta",
"ClinicalValidation.referenceFastaFai": "tests/data/reference.fasta.fai",
"ClinicalValidation.referenceFastaDict": "tests/data/reference.dict",
"ClinicalValidation.ignoreMaskedRef": true,
"ClinicalValidation.validationUnit": [
{
"callVcf": "tests/data/multisample.vcf.gz",
"baselineVcf": "tests/data/expected.vcf.gz",
"sampleNameVcf": "male",
"outputPrefix": "male-sample-output"
}
]
}
7 changes: 7 additions & 0 deletions tests/test_clinical_validation.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,3 +43,10 @@
- path: test-output/sample-output/calledSnps.vcf.gz
- path: test-output/sample-output/evalIndels/summary.txt
- path: test-output/sample-output/evalSNPs/summary.txt

- name: ignore-masked-ref
tags:
- integration
command: >-
cromwell run -o tests/cromwell_options.json
-i tests/integration/ignoreMaskedRef.json clinical-validation.wdl
10 changes: 10 additions & 0 deletions tests/test_sanity.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,13 @@
stdout:
contains:
- "Success!"

- name: womtool-ignore-masked-ref
tags:
- sanity
command: >-
womtool validate --inputs tests/integration/ignoreMaskedRef.json
clinical-validation.wdl
stdout:
contains:
- "Success!"