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wf_spurious_annot_pass2.cwl
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wf_spurious_annot_pass2.cwl
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#!/usr/bin/env cwl-runner
label: "spurious_annot pass2"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
inputs:
Extract_Model_Proteins_proteins: File
Extract_Model_Proteins_seqids: File
Extract_Model_Proteins_lds2: File
AntiFamLib: Directory
sequence_cache: Directory
Run_GeneMark_models: File
scatter_gather_nchunks: string
outputs:
AntiFam_tainted_proteins___oseqids:
type: File
outputSource: AntiFam_tainted_proteins/oseqids
Good_AntiFam_filtered_annotations_out:
type: File
outputSource: Good_AntiFam_filtered_annotations/out_annotation
Good_AntiFam_filtered_proteins_output:
type: File
outputSource: Good_AntiFam_filtered_proteins/output
steps:
Search_AntiFam:
label: "Search AntiFam"
run: ../task_types/tt_hmmsearch_wnode.cwl
in:
proteins: Extract_Model_Proteins_proteins
hmm_path: AntiFamLib
seqids: Extract_Model_Proteins_seqids
lds2: Extract_Model_Proteins_lds2
# hmms_tab: hmms_tab # goes eventually to -fam parameter -fam is empty here
asn_cache: sequence_cache
scatter_gather_nchunks: scatter_gather_nchunks
out: [hmm_hits]
AntiFam_tainted_proteins:
label: "AntiFam tainted proteins"
run: ../progs/reduce.cwl
in:
aligns: Search_AntiFam/hmm_hits
out: [oseqids] # this goes out as well
Good_AntiFam_filtered_proteins:
label: "Good, AntiFam filtered proteins"
run: ../progs/set_operation.cwl
in:
A:
source: [Extract_Model_Proteins_seqids]
linkMerge: merge_flattened
B:
source: [AntiFam_tainted_proteins/oseqids]
linkMerge: merge_flattened
operation:
default: '-' # subracts B from A
out: [output]
Good_AntiFam_filtered_annotations:
label: "Good, AntiFam filtered annotations"
run: ../progs/bact_filter_preserved.cwl
in:
# Run GeneMark bacterial_annot models ASNB_SEQ_ENTRY annotation
annotation: Run_GeneMark_models # -input
ifmt: # -ifmt
default: seq-entry
# Good, AntiFam filtered proteins spurious_annot gilist SEQID_LIST only_those_ids
only_those_ids: Good_AntiFam_filtered_proteins/output # -only-those-ids
nogenbank:
default: true
out: [out_annotation] # goes out -o