Workflow: bwa_se.cwl

Fetched 2021-01-14 04:58:41 GMT
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Inputs

ID Type Title Doc
job_uuid String
thread_count Long
readgroup_fastq_se https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/readgroup.yml#readgroup_fastq_se_file
reference_sequence File

Steps

ID Runs Label Doc
bwa_se
../../tools/bwa_record_se.cwl (CommandLineTool)
fastqc
../../tools/fastqc.cwl (CommandLineTool)
fastqc_db
../../tools/fastqc_db.cwl (CommandLineTool)
merge_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
readgroup_json_db
../../tools/readgroup_json_db.cwl (CommandLineTool)
bam_readgroup_to_json
../../tools/bam_readgroup_to_json.cwl (CommandLineTool)
fastqc_basicstats_json
../../tools/fastqc_basicstatistics_json.cwl (CommandLineTool)
merge_readgroup_json_db
../../tools/merge_sqlite.cwl (CommandLineTool)

Outputs

ID Type Label Doc
bam File
sqlite File
Permalink: https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/workflows/bamfastq_align/bwa_se.cwl