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tt_hmmsearch_wnode.cwl
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tt_hmmsearch_wnode.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
inputs:
hmm_path: Directory
proteins: File
seqids: File
lds2: File
hmms_tab: File?
asn_cache: Directory
scatter_gather_nchunks: string
outputs:
hmm_hits:
type: File
outputSource: collect_hmm_results/file_out
jobs:
type: File
outputSource: hmmsearch_create_jobs/jobs
workdir:
type: Directory
outputSource: hmmsearch_create_jobs/workdir
steps:
hmmsearch_create_jobs:
run: ../progs/hmmsearch_create_jobs.cwl
in:
hmm_path: hmm_path
seqids: seqids
out:
[jobs, workdir]
split_jobs:
run: ../split_jobs/split.cwl
in:
input: hmmsearch_create_jobs/jobs
nchunks: scatter_gather_nchunks
out: [ jobs ]
hmmsearch_wnode_qdump:
run: tt_hmmsearch_wnode_plus_qdump.cwl
scatter: input_jobs
in:
hmm_path: hmm_path
workdir: hmmsearch_create_jobs/workdir
proteins: proteins
lds2: lds2
asn_cache: asn_cache
hmms_tab: hmms_tab
input_jobs: split_jobs/jobs
out: [output]
collect_hmm_results:
run: ../split_jobs/cat_array_of_files.cwl
in:
files_in: hmmsearch_wnode_qdump/output
out: [ file_out ]