Workflow: metrics.cwl

Fetched 2019-12-07 04:19:05 GMT
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Inputs

ID Type Title Doc
job_uuid String
known_snp File
input_state String
parent_bam String
thread_count Long
fasta File
bam File

Steps

ID Runs Label Doc
picard_collectoxogmetrics_to_sqlite
../../tools/picard_collectoxogmetrics_to_sqlite.cwl (CommandLineTool)
picard_collectmultiplemetrics
../../tools/picard_collectmultiplemetrics.cwl (CommandLineTool)
picard_collectmultiplemetrics_to_sqlite
../../tools/picard_collectmultiplemetrics_to_sqlite.cwl (CommandLineTool)
samtools_idxstats
../../tools/samtools_idxstats.cwl (CommandLineTool)
picard_collectwgsmetrics
../../tools/picard_collectwgsmetrics.cwl (CommandLineTool)
samtools_idxstats_to_sqlite
../../tools/samtools_idxstats_to_sqlite.cwl (CommandLineTool)
picard_collectwgsmetrics_to_sqlite
../../tools/picard_collectwgsmetrics_to_sqlite.cwl (CommandLineTool)
picard_collectoxogmetrics
../../tools/picard_collectoxogmetrics.cwl (CommandLineTool)
samtools_flagstat_to_sqlite
../../tools/samtools_flagstat_to_sqlite.cwl (CommandLineTool)
samtools_flagstat
../../tools/samtools_flagstat.cwl (CommandLineTool)
merge_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
samtools_stats_to_sqlite
../../tools/samtools_stats_to_sqlite.cwl (CommandLineTool)
samtools_stats
../../tools/samtools_stats.cwl (CommandLineTool)

Outputs

ID Type Label Doc
merge_sqlite_destination_sqlite File
Permalink: https://w3id.org/cwl/view/git/58af8583ab04b8836777745a2116a2e79f9b441b/workflows/dnaseq/metrics.cwl