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wf_spurious_annot_pass1.cwl
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wf_spurious_annot_pass1.cwl
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#!/usr/bin/env cwl-runner
label: spurious_annot
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
inputs:
Extract_ORF_Proteins_proteins: File
Extract_ORF_Proteins_seqids: File
Extract_ORF_Proteins_lds2: File
AntiFamLib: Directory
sequence_cache: Directory
outputs:
AntiFam_tainted_proteins_I___oseqids:
type: File
outputSource: AntiFam_tainted_proteins_I/oseqids
steps:
Search_AntiFam_I:
label: "Search AntiFam I"
run: ../task_types/tt_hmmsearch_wnode.cwl
in:
proteins: Extract_ORF_Proteins_proteins
hmm_path: AntiFamLib
seqids: Extract_ORF_Proteins_seqids
lds2: Extract_ORF_Proteins_lds2
# hmms_tab: hmms_tab # goes eventually to -fam parameter -fam is empty here
asn_cache: sequence_cache
out: [hmm_hits]
AntiFam_tainted_proteins_I:
label: "AntiFam tainted proteins I"
run: ../progs/reduce.cwl
in:
aligns: Search_AntiFam_I/hmm_hits
out: [oseqids] # this goes out as well
#### this node does nothing
# Good,_AntiFam_filtered_proteins_I:
# label: "Good, AntiFam filtered proteins I"
# run: ../progs/set_operation.cwl
# in:
# A:
# source: [Extract_ORF_Proteins_seqids]
# linkMerge: merge_flattened
# B:
# source: [AntiFam_tainted_proteins_I/seqids]
# linkMerge: merge_flattened
# operation:
# default: '-' # subracts B from A
# out: [output] # does not go out