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Changing variable name in MT WDL to match gatk-workflows #5694

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Merged
merged 1 commit into from
Feb 21, 2019
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Changing variable name in MT WDL to match gatk-workflows #5694

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2 changes: 1 addition & 1 deletion scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"MitochondriaPipeline.wgs_aligned_input_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam",
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam",
"MitochondriaPipeline.autosomal_coverage": 30,
"MitochondriaPipeline.MT_with_numts_intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/chrMWithFinalNuMTs.hg38.interval_list",
"MitochondriaPipeline.mt_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.dict",
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2 changes: 1 addition & 1 deletion scripts/mitochondria_m2_wdl/ExampleInputsMitochondriaPipeline.json
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"MitochondriaPipeline.wgs_aligned_input_bam": "input_bam_here",
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "input_bam_here",
"MitochondriaPipeline.autosomal_coverage": autosomal_median_coverage_here,
"MitochondriaPipeline.MT_with_numts_intervals": "gs://broad-references/hg38/v0/chrM/chrMWithFinalNuMTs.hg38.interval_list",
"MitochondriaPipeline.mt_dict": "gs://broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.dict",
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4 changes: 2 additions & 2 deletions scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
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Expand Up @@ -11,7 +11,7 @@ workflow MitochondriaPipeline {
autosomal_coverage: "Median coverage of full input bam"
out_vcf: "Final VCF of mitochondrial SNPs and INDELs"
}
File wgs_aligned_input_bam
File wgs_aligned_input_bam_or_cram
Int? autosomal_coverage

File MT_with_numts_intervals
Expand Down Expand Up @@ -65,7 +65,7 @@ workflow MitochondriaPipeline {

call SubsetBam {
input:
input_bam = wgs_aligned_input_bam,
input_bam = wgs_aligned_input_bam_or_cram,
interval_list = MT_with_numts_intervals,
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
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