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gp_makeblastdb.cwl
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gp_makeblastdb.cwl
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cwlVersion: v1.0
label: "gp_makeblastdb"
class: Workflow
requirements:
- class: StepInputExpressionRequirement
inputs:
asn_cache: Directory[]
asnb: File?
asnt: File?
dbtype: string
fasta: File?
hardmask: File?
softmask: File?
title: string
ids: File?
steps:
actual:
run:
class: CommandLineTool
baseCommand: gp_makeblastdb
arguments: [ -nogenbank ]
inputs:
asn_cache:
type: Directory[]
inputBinding:
prefix: -asn-cache
itemSeparator: ","
asnb:
type: File?
inputBinding:
prefix: -asnb
asnt:
type: File?
inputBinding:
prefix: -asnt
dbtype:
type: string
inputBinding:
prefix: -dbtype
fasta:
type: File?
inputBinding:
prefix: -fasta
found_ids_output_file: # -found-ids-output out/found_ids.txt \
type: string
default: found_ids.txt
inputBinding:
prefix: -found-ids-output
found_ids_output_manifest: # -found-ids-output-manifest out/found_ids.mft \
type: string
default: found_ids.mft
inputBinding:
prefix: -found-ids-output-manifest
hardmask: # -hardmask-manifest inp/hardmask_data.mft
type: File?
inputBinding:
prefix: -hardmask
output_db_file:
type: string
default: blastdb
inputBinding:
prefix: -db
output_db_manifest:
type: string
default: blastdb.mft
inputBinding:
prefix: -output-manifest
softmask: # -softmask-manifest inp/softmask_data.mft \
type: File?
inputBinding:
prefix: -softmask
title: # -title 'BLASTdb created by GPipe'
type: string
inputBinding:
prefix: -title
ids:
type: File?
inputBinding:
prefix: -ids
outputs:
dbname:
type: string
outputBinding:
outputEval: $(inputs.output_db_file)
found_ids:
type: File
outputBinding:
glob: $(inputs.found_ids_output_file)
blastfiles:
type: File[]
outputBinding:
glob: "blastdb.*" # string literal here must match ${output_db_file}
in:
asn_cache: asn_cache
asnb: asnb
asnt: asnt
dbtype: dbtype
fasta: fasta
hardmask: hardmask # -hardmask-manifest inp/hardmask_data.mft
softmask: softmask # -softmask-manifest inp/softmask_data.mft \
title: title # -title 'BLASTdb created by GPipe'
ids: ids
out: [blastfiles]
mkdir:
run:
class: CommandLineTool
requirements:
- class: ShellCommandRequirement
arguments:
- shellQuote: false
valueFrom: >-
mkdir $(inputs.blastdir) && cp
inputs:
blastfiles:
type: File[]
inputBinding:
position: 1
blastdir:
type: string
inputBinding:
position: 2
outputs:
blastdb:
type: Directory
outputBinding:
glob: $(inputs.blastdir)
in:
blastfiles: actual/blastfiles
blastdir:
default: blastdir
out: [blastdb]
outputs:
blastdb:
type: Directory
outputSource: mkdir/blastdb