/
wf_genomic_source_asn.cwl
executable file
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/
wf_genomic_source_asn.cwl
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#!/usr/bin/env cwl-runner
label: "Create Genomic Collection for Bacterial Pipeline, ASN.1 input"
cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
inputs:
entries: File?
seq_submit: File?
# taxid: int
gc_assm_name: string
taxon_db: File
outputs:
ids_out:
type: File
outputSource: Cache_Seq_entries/oseq_ids
asncache:
type: Directory
outputSource: Cache_Seq_entries/asn_cache
gencoll_asn:
type: File
outputSource: Create_Assembly_From_Sequences/gencoll_asn
seqid_list:
type: File
outputSource: Extract_Assembly_Information/seqid_list
stats_report:
type: File
outputSource: Extract_Assembly_Information_XML/stats_report
submit_block_template:
type: File
outputSource: Prepare_Seq_entries/submit_block
steps:
Prepare_Seq_entries:
run: ../progs/prepare_seq_entry_input.cwl
in:
entries: entries
seq_submit: seq_submit
out: [order, submit_block, output_entries]
Cache_Seq_entries:
run: ../progs/prime_cache.cwl
in:
input: Prepare_Seq_entries/output_entries
taxon_db: taxon_db
# taxid: taxid
ifmt:
default: asn-seq-entry
out: [oseq_ids, asn_cache]
Create_Assembly_From_Sequences:
run: gc_create.cwl
in:
unplaced: Cache_Seq_entries/oseq_ids
asn_cache: Cache_Seq_entries/asn_cache
gc_assm_name: gc_assm_name
out: [gencoll_asn]
Extract_Assembly_Information:
run: gc_get_molecules.cwl
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]