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vecscreen.cwl
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vecscreen.cwl
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class: Workflow
cwlVersion: v1.0
id: vecscreen
label: vecscreen
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
- id: adaptor_fasta
type: File
- id: contam_in_prok_blastdb_dir
type: Directory
- id: contig_fasta
type: File
- id: ignore_all_errors
type: boolean?
steps:
default_plane:
run: ../vecscreen/foreign_screening.cwl
label: foreign_screening
doc: >-
corresponds to part of default plane in foreign contamination screening
graph of classic Gpipe
it does bunch of generic things so it has to be first
in:
adaptor_fasta: adaptor_fasta
contig_fasta: contig_fasta
out: [adaptor_blastdb_dir, contig_ids_out, feats, hits, out_cache_dir]
bacterial_screening:
run: ../vecscreen/bacterial_screening.cwl
label: bacterial_screening
doc: >-
corresponds to bacterial_screening plane in in foreign contamination
screening graph of classic Gpipe
in:
asn_cache: default_plane/out_cache_dir
contam_in_prok_blastdb_dir: contam_in_prok_blastdb_dir
contig_gilist: default_plane/contig_ids_out
out: [blast_align, feats, filtered_align]
FSCR_Calls_first_pass:
run: ../task_types/tt_fscr_calls_pass1.cwl
in:
contigs: default_plane/contig_ids_out
input: [bacterial_screening/feats, default_plane/feats]
asn_cache: default_plane/out_cache_dir
out: [calls]
doc: >-
corresponds to part of default plane in foreign contamination screening
graph of classic Gpipe
it should go _after_ all screenings, so it goes to a separate degenerate
"plane" = "task" here
screen_evaluate:
run: ../progs/screen_evaluate.cwl
in:
tab: FSCR_Calls_first_pass/calls
ifmt:
default: seq-annot
ignore_all_errors: ignore_all_errors
out: [success]
outputs:
out_cache_dir:
type: Directory
outputSource: default_plane/out_cache_dir
contamination_feats:
type: File
outputSource: bacterial_screening/feats
foreign_feats:
type: File
outputSource: default_plane/feats
blast_align:
type: File
outputSource: bacterial_screening/blast_align
filtered_align:
type: File
outputSource: bacterial_screening/filtered_align
hits:
type: File
outputSource: default_plane/hits
adaptor_blastdb_dir:
type: Directory
outputSource: default_plane/adaptor_blastdb_dir
calls:
type: File
outputSource: FSCR_Calls_first_pass/calls
success:
type: boolean
outputSource: screen_evaluate/success