/
wf_trnascan.cwl
executable file
·91 lines (87 loc) · 2.14 KB
/
wf_trnascan.cwl
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#!/usr/bin/env cwl-runner
label: "Run tRNAScan"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
inputs:
go:
type: boolean[]
asn_cache: Directory
seqids: File
taxid: int
taxon_db: File
scatter_gather_nchunks: string
outputs:
annots:
type: File
outputSource: Run_tRNAScan_trnascan_dump/outasn
steps:
Run_tRNAScan_submit:
run: gpx_qsubmit_trnascan.cwl
in:
asn_cache: asn_cache
seqids: seqids
#out: [asncache, jobs]
out: [jobs]
Compute_Gencode_for_trna:
run: ../progs/compute_gencode.cwl
in:
taxid: taxid
taxon_db: taxon_db
gencode:
default: true
out: [ output ]
Compute_Superkingdom_for_trna:
run: ../progs/compute_gencode.cwl
in:
taxid: taxid
taxon_db: taxon_db
superkingdom:
default: true
out: [ output ]
Compute_Gencode_int_for_trna:
run: ../progs/file2int.cwl
in:
input: Compute_Gencode_for_trna/output
out: [ value ]
Compute_Superkingdom_int_for_trna:
run: ../progs/file2int.cwl
in:
input: Compute_Superkingdom_for_trna/output
out: [ value ]
Get_TRNA_model:
run: ../progs/gencode2trnamodel.cwl
in:
gencode: Compute_Gencode_int_for_trna/value
out: [output]
split_jobs:
run: ../split_jobs/split.cwl
in:
input: Run_tRNAScan_submit/jobs
nchunks: scatter_gather_nchunks
# chunk_size: scatter_gather_chunk_size
out: [ jobs ]
Run_scan_and_dump:
run: wf_scan_and_dump.cwl
scatter: input_jobs
in:
asn_cache: asn_cache
input_jobs: split_jobs/jobs
#input_jobs: jobs
taxid: taxid
gcode_othmito: Get_TRNA_model/output
taxon_db: taxon_db
superkingdom: Compute_Superkingdom_int_for_trna/value
out: [intermediate]
collect_intermediate:
run: ../split_jobs/cat_array_of_files.cwl
in:
files_in: Run_scan_and_dump/intermediate
out: [ file_out ]
Run_tRNAScan_trnascan_dump:
run: trnascan_dump.cwl
in:
input: collect_intermediate/file_out
out: [outasn, outstruct]