Workflow: alignment_bwa_mem_no_trim.cwl

Fetched 2021-03-04 15:35:22 GMT
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Inputs

ID Type Title Doc
reference File
job_uuid String
readgroup_names String[]
interval_bed File
input_read2 File[]
input_read1 File[]
readgroup_lines String[]

Steps

ID Runs Label Doc
bam_reheader
../../tools/harmonization/samtools_filter_reheader.cwl (CommandLineTool)
readgroups_merge
../../tools/harmonization/sambamba_merge.cwl (CommandLineTool)
bwa_mem_filter_dedup
../../tools/harmonization/bwa_mem.cwl (CommandLineTool)
get_bam_new_header
../../tools/harmonization/get_bam_new_header.cwl (CommandLineTool)
bam_sort
../../tools/harmonization/sambamba_sort.cwl (CommandLineTool)

Outputs

ID Type Label Doc
time_metrics_from_sort File
sorted_bam File
time_metrics_from_reheader File
time_metrics_from_merge File
time_metrics_from_bwa_mem_filter_dedup File[]
Permalink: https://w3id.org/cwl/view/git/28bb82ba031041321ff9caa5c299ec1bb15d7471/genomel/cwl/workflows/harmonization/alignment_bwa_mem_no_trim.cwl