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wf_pgap_simple.cwl
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wf_pgap_simple.cwl
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#!/usr/bin/env cwl-runner
label: "PGAP Pipeline, simple user input"
cwlVersion: v1.0
class: Workflow
doc: |
PGAP pipeline for external usage, powered via containers,
simple user input: (FASTA + yaml only, no template)
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
#
# User specified input for "standard" (wf_pgap.cwl) workflow
#
fasta: File
submit_block_template: File
taxid: int
gc_assm_name: string
report_usage: boolean
#
# User specified input for "simple user input" case (this)
#
tech: string?
completeness: string?
#
# User independent, static input for "standard" (wf_pgap.cwl) workflow
#
blast_rules_db:
type: string
default: blast_rules_db
supplemental_data:
type: Directory
default:
class: Directory
location: input
# hmm_path: Directory
# hmms_tab: File
# naming_hmms_tab: File
# uniColl_cache: Directory
# gene_master_ini: File
# 16s_blastdb_dir: Directory
# 23s_blastdb_dir: Directory
# 5s_model_path: File
# rfam_model_path: File
# rfam_amendments: File
# rfam_stockholm: File
# AntiFamLib: Directory
# blast_rules_db_dir: Directory
# thresholds: File
# naming_sqlite: File
# selenoproteins: Directory
# naming_hmms_combined: Directory
# wp_hashes: File
# taxon_db: File
# genemark_path: Directory
# naming_blast_db: Directory
# CDDdata: Directory
# CDDdata2: Directory
# defline_cleanup_rules: File
# univ_prot_xml: File
# val_res_den_xml: File
# asn2pas_xsl: File
#
# User independent, static input for "simple user input" case (this)
#
submit_block_template_static: File
molinfo_complete_asn: File
molinfo_wgs_asn: File
steps:
prepare_input_template:
run: prepare_user_input.cwl
in:
tech: tech
completeness: completeness
submit_block_template_static: submit_block_template_static
molinfo_complete_asn: molinfo_complete_asn
molinfo_wgs_asn: molinfo_wgs_asn
out: [submit_block_template]
standard_pgap:
run: wf_common.cwl
in:
#fasta: fasta
#submit_block_template: prepare_input_template/submit_block_template
taxid: taxid
gc_assm_name: gc_assm_name
report_usage: report_usage
supplemental_data: supplemental_data
blast_rules_db: blast_rules_db
# hmm_path: hmm_path
# hmms_tab: hmms_tab
# naming_hmms_tab: naming_hmms_tab
# uniColl_cache: uniColl_cache
# gene_master_ini: gene_master_ini
# 16s_blastdb_dir: 16s_blastdb_dir
# 23s_blastdb_dir: 23s_blastdb_dir
# 5s_model_path: 5s_model_path
# rfam_model_path: rfam_model_path
# rfam_amendments: rfam_amendments
# rfam_stockholm: rfam_stockholm
# AntiFamLib: AntiFamLib
# blast_rules_db_dir: blast_rules_db_dir
# thresholds: thresholds
# naming_sqlite: naming_sqlite
# selenoproteins: selenoproteins
# naming_hmms_combined: naming_hmms_combined
# wp_hashes: wp_hashes
# taxon_db: taxon_db
# genemark_path: genemark_path
# naming_blast_db: naming_blast_db
# CDDdata: CDDdata
# CDDdata2: CDDdata2
# defline_cleanup_rules: defline_cleanup_rules
# univ_prot_xml: univ_prot_xml
# val_res_den_xml: val_res_den_xml
# asn2pas_xsl: asn2pas_xsl
out: [gbent, gff, gbk, nucleotide_fasta, protein_fasta]
outputs:
gbent:
type: File
outputSource: standard_pgap/gbent
gff:
type: File
outputSource: standard_pgap/gff
gbk:
type: File
outputSource: standard_pgap/gbk
nucleotide_fasta:
type: File?
outputSource: standard_pgap/nucleotide_fasta
protein_fasta:
type: File?
outputSource: standard_pgap/protein_fasta