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wf_bacterial_annot_pass1.cwl
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wf_bacterial_annot_pass1.cwl
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#!/usr/bin/env cwl-runner
label: "Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
go:
type: boolean[]
asn_cache: Directory
inseq: File
hmm_path: Directory
hmms_tab: File
uniColl_cache: Directory
trna_annots: File
ncrna_annots: File
nogenbank: boolean
Execute_CRISPRs_annots: File
Generate_16S_rRNA_Annotation_annotation: File
Generate_23S_rRNA_Annotation_annotation: File
Post_process_CMsearch_annotations_annots_5S: File
thresholds: File
genemark_path: Directory
# Cached computational steps
#hmm_hits: File
scatter_gather_nchunks: string
outputs:
outseqs:
type: File
outputSource: Get_ORFs/outseqs
aligns:
type: File
outputSource: Map_HMM_Hits/aligns
hmm_hits:
type: File
outputSource: Search_All_HMMs_I/hmm_hits
proteins:
type: File
outputSource: Extract_ORF_Proteins/proteins
lds2:
type: File
outputSource: Extract_ORF_Proteins/lds2
seqids:
type: File
outputSource: Extract_ORF_Proteins/seqids
prot_ids:
type: File
outputSource: Get_off_frame_ORFs/prot_ids
protein_aligns:
type: File
outputSource: Resolve_Annotation_Conflicts/protein_aligns
annotation:
type: File
outputSource: Resolve_Annotation_Conflicts/annotation
out_hmm_params:
type: File
outputSource: Run_GeneMark_Training/out_hmm_params
steps:
Get_ORFs:
run: ../progs/gp_getorf.cwl
in:
asn_cache: asn_cache
input: inseq
out: [outseqs]
Extract_ORF_Proteins:
run: ../progs/protein_extract.cwl
in:
input: Get_ORFs/outseqs
nogenbank: nogenbank
out: [proteins, lds2, seqids]
# Skipped due to compute cost, for now
Search_All_HMMs_I:
label: "Search All HMMs I"
run: ../task_types/tt_hmmsearch_wnode.cwl
in:
proteins: Extract_ORF_Proteins/proteins
hmm_path: hmm_path
seqids: Extract_ORF_Proteins/seqids
lds2: Extract_ORF_Proteins/lds2
hmms_tab: hmms_tab
asn_cache: asn_cache
scatter_gather_nchunks: scatter_gather_nchunks
out:
[hmm_hits]
#[hmm_hits, jobs, workdir]
Map_HMM_Hits:
run: bacterial_hit_mapping.cwl
in:
seq_cache: asn_cache
unicoll_cache: uniColl_cache
asn_cache: [asn_cache, uniColl_cache]
# hmm_hits: hmm_hits # Should be from hmmsearch
hmm_hits: Search_All_HMMs_I/hmm_hits
sequences: Get_ORFs/outseqs
### this guys below not tested yet
align_fmt:
default: seq-align
expansion_ratio:
default: 0.0
no_compart:
default: true
nogenbank:
default: true
out: [aligns]
Get_off_frame_ORFs:
run: get_off_frame_orfs.cwl
label: "Get_off_frame_ORFs task node"
in:
aligns: Map_HMM_Hits/aligns
seq_entries: Get_ORFs/outseqs
out: [prot_ids]
Resolve_Annotation_Conflicts:
label: "Resolve Annotation Conflicts"
run: ../progs/bacterial_resolve_conflicts.cwl
in:
features: # all external to this node
- Execute_CRISPRs_annots # Execute CRISPR/annots
- ncrna_annots # Post-process CMsearch Rfam annotations/annots
- Generate_16S_rRNA_Annotation_annotation # Generate 16S rRNA Annotation/annotation
- Generate_23S_rRNA_Annotation_annotation # Generate 23S rRNA Annotation/annotation
- Post_process_CMsearch_annotations_annots_5S # Post-process CMsearch annotations/annots
- trna_annots # Run tRNAScan/annot
# input_annotation: mft not used
# prot: mft not used
# mapped-regions: mft not used
thr: thresholds
asn_cache:
source: [asn_cache]
linkMerge: merge_flattened
out:
- protein_aligns
- annotation
Run_GeneMark_Training:
label: "Run GeneMark Training, genemark"
run: ../progs/genemark_training.cwl
in:
asn_cache:
source: [asn_cache, uniColl_cache]
linkMerge: merge_flattened
sequences: inseq
genemark_path: genemark_path # ${GP_HOME}/third-party/GeneMark
marked_annotation_name:
default: marked-annotation.asn
min_seq_len:
default: 200
preliminary_models_name: # -out
default: preliminary-models.asn
thr: thresholds
tmp_dir_name:
default: workdir
# type: Directory
nogenbank:
default: true
out: [out_hmm_params] # export