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wf_protein_alignment.cwl
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wf_protein_alignment.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
label: "Align reference proteins plane complete workflow"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
go:
type: boolean[]
asn_cache: Directory
uniColl_asn_cache: Directory
blastdb_dir: Directory # genomic
taxid: int
tax_sql_file: File
gc_assembly: File
compartments: File
all_prots: File
outputs:
align:
type: File
outputSource: Filter_Protein_Alignments/align
align_non_match:
type: File
outputSource: Filter_Protein_Alignments/align_non_match
steps:
Compute_Gencode:
run: ../progs/compute_gencode.cwl
in:
taxid: taxid
taxon_db: tax_sql_file
gencode:
default: true
out: [ output ]
Compute_Gencode_int:
run: ../progs/file2int.cwl
in:
input: Compute_Gencode/output
out: [ value ]
Seed_Search_Compartments:
run: wf_seed.cwl
in:
db_gencode: Compute_Gencode_int/value
asn_cache: asn_cache
uniColl_asn_cache: uniColl_asn_cache
compartments: compartments
out: [ blast_align ]
Seed_Protein_Alignments:
run: wf_seed_1.cwl
in:
db_gencode: Compute_Gencode_int/value
asn_cache: asn_cache
uniColl_asn_cache: uniColl_asn_cache
seqids: all_prots # Get_Proteins/all_prots
blastdb_dir: blastdb_dir
out: [ blast_align ]
cat:
run: cat.cwl
in:
file_in_1: Seed_Protein_Alignments/blast_align
file_in_2: Seed_Search_Compartments/blast_align
out: [ file_out ]
Sort_Seed_Hits:
run: align_sort.cwl
in:
asn_cache: asn_cache
uniColl_asn_cache: uniColl_asn_cache
blast_aligns: cat/file_out
limit_mem:
default: '1G'
out: [ sorted_aligns ]
Filter_Full_Coverage_Alignments:
run: bacterial_protalign_filter.cwl
in:
asn_cache: asn_cache
uniColl_asn_cache: uniColl_asn_cache
sorted_seeds: Sort_Seed_Hits/sorted_aligns
out: [ blast_full_cov, blast_partial_cov ]
compart_filter_prosplign:
run: wf_compart_filter_prosplign.cwl
in:
asn_cache: asn_cache
uniColl_asn_cache: uniColl_asn_cache
seed_hits: Filter_Full_Coverage_Alignments/blast_partial_cov
gc_assembly: gc_assembly
out: [ prosplign_align ]
Filter_Protein_Alignments:
run: wf_align_filter.cwl
in:
asn_cache: asn_cache
uniColl_asn_cache: uniColl_asn_cache
blast_full: Filter_Full_Coverage_Alignments/blast_full_cov
prosplign: compart_filter_prosplign/prosplign_align
out: [ align, align_non_match ]