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Fix output_bam_basename calculation #5

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Fix output_bam_basename calculation #5

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a5fa753
Made ref_alt optional as a workflow parameter
multimeric Oct 18, 2018
6edbea7
Merge branch 'master' of github.com:gatk-workflows/gatk3-data-processing
multimeric Feb 19, 2019
ed26df5
Use basename instead of sub()ing out the url prefix
multimeric Feb 19, 2019
f94f069
Use an intermediate variable for the BAM basename
multimeric Feb 19, 2019
055b852
Removed unused comment
multimeric Feb 19, 2019
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12 changes: 4 additions & 8 deletions processing-for-variant-discovery-gatk3.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -76,18 +76,14 @@ workflow GenericPreProcessingWorkflow {
# Align flowcell-level unmapped input bams in parallel
scatter (unmapped_bam in flowcell_unmapped_bams) {

# Because of a wdl/cromwell bug this is not currently valid so we have to sub(sub()) in each task
# String base_name = sub(sub(unmapped_bam, "gs://.*/", ""), unmapped_bam_suffix + "$", "")

String sub_strip_path = "gs://.*/"
String sub_strip_unmapped = unmapped_bam_suffix + "$"
String base_name = sub(basename(unmapped_bam), unmapped_bam_suffix + "$", "") + ".unmerged"

# Map reads to reference
call SamToFastqAndBwaMem {
input:
input_bam = unmapped_bam,
bwa_commandline = bwa_commandline,
output_bam_basename = sub(sub(unmapped_bam, sub_strip_path, ""), sub_strip_unmapped, "") + ".unmerged",
output_bam_basename = base_name,
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
ref_dict = ref_dict,
Expand All @@ -108,7 +104,7 @@ workflow GenericPreProcessingWorkflow {
bwa_commandline = bwa_commandline,
bwa_version = GetBwaVersion.version,
aligned_bam = SamToFastqAndBwaMem.output_bam,
output_bam_basename = sub(sub(unmapped_bam, sub_strip_path, ""), sub_strip_unmapped, "") + ".aligned.unsorted",
output_bam_basename = base_name,
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
ref_dict = ref_dict,
Expand All @@ -120,7 +116,7 @@ workflow GenericPreProcessingWorkflow {
call SortAndFixTags as SortAndFixReadGroupBam {
input:
input_bam = MergeBamAlignment.output_bam,
output_bam_basename = sub(sub(unmapped_bam, sub_strip_path, ""), sub_strip_unmapped, "") + ".sorted",
output_bam_basename = base_name,
ref_dict = ref_dict,
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
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