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sidearm.cwl
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sidearm.cwl
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#!/usr/bin/env cwl-runner --preserve-environment BLASTDB --preserve-environment PERL5LIB
cwlVersion: v1.0
class: Workflow
inputs:
# align
srr: string
blastdb: string
threads: int
# bam2seqs
seqformat: string
nopaired: boolean
# summarize_bam_by_ref
accver: boolean?
genomefile: File
# trim
prime5: string?
prime3: string?
outputs:
bamfile:
type: File
outputSource: alignsrr/outputfile
report_tsv:
type: File
outputSource: summarizebam/outputfile
trimlog:
type: File
outputSource: trim/logfile
trimseqs:
type: File
outputSource: trim/outputfile
assemblylog:
type: File
outputSource: assembly/logfile
viral_contigs:
type: File
outputSource: assembly/contigs
steps:
alignsrr:
run: align_SRR_to_references.cwl
in:
srr: srr
blastdb: blastdb
threads: threads
out: [outputfile]
summarizebam:
run: summarize_bam_by_ref.cwl
in:
bamfile: alignsrr/outputfile
genomefile: genomefile
accver: accver
out: [outputfile]
bam2seqs:
run: bam2seqs.cwl
in:
bamfile: alignsrr/outputfile
seqformat: seqformat
nopaired: nopaired
out: [outputfile]
trim:
run: trim.cwl
in:
seqs: bam2seqs/outputfile
out: [outputfile, logfile]
assembly:
run: assembly.cwl
in:
seqs: trim/outputfile
out: [contigs, logfile]