/
wf_genomic_source.cwl
executable file
·87 lines (75 loc) · 2.46 KB
/
wf_genomic_source.cwl
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#!/usr/bin/env cwl-runner
label: "Create Genomic Collection for Bacterial Pipeline"
cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
inputs:
fasta: File
taxid: int
gc_assm_name: string
taxon_db: File
submit_block_template: File
# sequence_cache_shortcut: Directory
# ids_out_shortcut: File
outputs:
ids_out:
type: File
outputSource: Cache_FASTA_Sequences/oseq_ids
# outputSource: ids_out_shortcut
asncache:
type: Directory
outputSource: Cache_FASTA_Sequences/asn_cache
# outputSource: sequence_cache_shortcut # this is over when GP-24223 is resolved
gencoll_asn:
type: File
outputSource: Create_Assembly_From_Sequences/gencoll_asn
seqid_list:
#type: File[]
type: File
outputSource: Extract_Assembly_Information/seqid_list
stats_report:
type: File
outputSource: Extract_Assembly_Information_XML/stats_report
steps:
#### waiting for GP-24223
#### commented out
Cache_FASTA_Sequences:
run: ../progs/prime_cache.cwl
in:
input: fasta
taxon_db: taxon_db
taxid: taxid
submit_block_template: submit_block_template
out: [oseq_ids, asn_cache]
Create_Assembly_From_Sequences:
run: gc_create.cwl
in:
unplaced: Cache_FASTA_Sequences/oseq_ids # waiting for GP-24223
# unplaced: ids_out_shortcut # waiting for GP-24223
asn_cache: Cache_FASTA_Sequences/asn_cache # waiting for GP-24223
# asn_cache: sequence_cache_shortcut # waiting for GP-24223
gc_assm_name: gc_assm_name
out: [gencoll_asn]
Extract_Assembly_Information:
run: gc_get_molecules.cwl
#
# In Classic PGAP we call this many times to produce all kind of filtered output, while
# using only one filtered output: reference-no-organelle downstream
#
#scatter: [ filter, outfile ]
#scatterMethod: dotproduct
in:
gc_assembly: Create_Assembly_From_Sequences/gencoll_asn
filter:
#default: ["all", "all-no-organelle", "non-reference-no-organelle", "organelle", "reference-no-organelle"]
default: "reference-no-organelle"
outfile:
#default: ["all.gi", "no_organelle.gi", "no_ref_no_organelle.gi", "organelle.gi", "ref_no_organelle.gi"]
default: "ref_no_organelle.gi"
out: [seqid_list]
Extract_Assembly_Information_XML:
run: gc_asm_xml_description.cwl
in:
asnfile: Create_Assembly_From_Sequences/gencoll_asn
out: [stats_report]