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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
# make a workflow with jobs.xml as an input and a single file as an output to apply scatter/gather
label: "cluster_blastp_wnode and gpx_qdump combined"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
input_jobs: File
blastdb_dir: Directory[]
lds2: File
proteins: File
asn_cache: Directory[]
nogenbank: boolean
align_filter: string
allow_intersection: boolean
comp_based_stats: string # F/T
compart: boolean
dbsize: string # can't int, because too large
evalue: float?
extra_coverage: int?
max_jobs: int
max_target_seqs: int
no_merge: boolean
ofmt: string
seg: string
threshold: int
top_by_score: int
word_size: int
outputs:
blast_align:
type: File
outputSource: gpx_qdump/output
steps:
cluster_blastp_wnode:
run: ../progs/cluster_blastp_wnode.cwl
in:
input_jobs: input_jobs
align_filter: align_filter
allow_intersection: allow_intersection
asn_cache: asn_cache
blastdb_dir: blastdb_dir
comp_based_stats: comp_based_stats
compart: compart
dbsize: dbsize
evalue: evalue
extra_coverage: extra_coverage
lds2: lds2
proteins: proteins # companion to lds2
max_jobs: max_jobs
max_target_seqs: max_target_seqs
no_merge: no_merge
nogenbank: nogenbank
ofmt: ofmt
seg: seg
threshold: threshold
top_by_score: top_by_score
word_size: word_size
workers_per_cpu:
default: 1.0
out: [outdir]
gpx_qdump:
run: ../progs/gpx_qdump.cwl
in:
input_path: cluster_blastp_wnode/outdir # production mode
unzip:
default: '*'
out: [ output ]
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