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wf_bacterial_annot_pass3.cwl
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wf_bacterial_annot_pass3.cwl
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#!/usr/bin/env cwl-runner
label: "Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
AntiFamLib:
type: Directory
uniColl_cache:
type: Directory
sequence_cache:
type: Directory
hmm_aligns:
type: File
label: "Map HMM Hits/align"
prot_aligns:
type: File
label: "Filter Protein Alignments I/align"
annotation:
type: File
label: "Resolve Annotation Conflicts/annotation"
models1:
type: File
label: "Run GeneMark Training/models"
raw_seqs:
type: File
label: #Prepare Unannotated Sequences/raw_seqs"
thresholds: # ${GP_HOME}/etc/thresholds.xml
type: File
naming_sqlite: # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/third-party/data/BacterialPipeline/uniColl/ver-3.2/naming.sqlite
type: File
hmm_params: # Run GeneMark Training/hmm_params (EXTERNAL, put to input/
type: File?
selenoproteins: # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/third-party/data/BacterialPipeline/Selenoproteins/selenoproteins
type: Directory
selenocysteines_db:
type: string
default: blastdb
naming_hmms_combined: # ${GP_HOME}/third-party/data/BacterialPipeline/uniColl/ver-3.2/naming_hmms_combined.mft
type: Directory
hmms_tab:
type: File
wp_hashes: File # input/wp-hashes.sqlite
taxon_db: File # input/taxonomy.sqlite3
genemark_path: Directory
scatter_gather_nchunks: string
steps:
Extract_ab_initio_Proteins:
label: "Extract ab initio Proteins"
run: ../progs/protein_extract.cwl
in:
input: models1
nogenbank:
default: true
out: [proteins, lds2, seqids]
Search_ab_initio_for_AntiFam:
label: "Search ab initio for AntiFam"
run: ../task_types/tt_hmmsearch_wnode.cwl
in:
# this comes always with lds2. LDS2 refers to proteins
proteins: Extract_ab_initio_Proteins/proteins
hmm_path: AntiFamLib
seqids: Extract_ab_initio_Proteins/seqids
lds2: Extract_ab_initio_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]
ab_initio_AntiFam_tainted_proteins:
label: "ab initio AntiFam tainted proteins"
run: ../progs/reduce.cwl
in:
aligns: Search_ab_initio_for_AntiFam/hmm_hits
out: [oseqids]
Good_ab_initio_proteins:
label: "Good ab initio proteins"
run: ../progs/set_operation.cwl
in:
A:
source: [Extract_ab_initio_Proteins/seqids]
linkMerge: merge_flattened
B:
source: [ab_initio_AntiFam_tainted_proteins/oseqids]
linkMerge: merge_flattened
operation:
default: '-' # subracts B from A
out: [output]
Good_ab_initio_annotations:
label: "Good ab initio annotations"
run: ../progs/bact_filter_preserved.cwl
in:
annotation: models1
ifmt:
default: seq-entry
only_those_ids: Good_ab_initio_proteins/output
nogenbank:
default: true
out: [out_annotation] # goes out -o
Find_Best_Evidence_Alignments:
label: "Find Best Evidence Alignments"
run: ../progs/bact_best_evidence_alignments.cwl
in:
annotation: [annotation, Good_ab_initio_annotations/out_annotation]
asn_cache: [uniColl_cache, sequence_cache] # ${GP_cache_dir},${GP_HOME}/third-party/data/BacterialPipeline/uniColl/ver-3.2/cache
# type: Directory[]
align: [hmm_aligns, prot_aligns] # -input-manifest
# type: File[]
# source:
# linkMerge: merge_flattened
max_overlap:
default: 120
output_align_name:
default: best_aligns.asn
start_stop_allowance:
default: 60
thr: thresholds
unicoll_sqlite: naming_sqlite
nogenbank:
default: true
out: [out_align] # -o
Run_GeneMark:
label: "Run GeneMark"
run: ../progs/genemark.cwl
in: # so far, the whole node!
alignments: Find_Best_Evidence_Alignments/out_align
annotation: annotation # Resolve Annotation Conflicts/annotation (EXTERNAL, put to input/
asn_cache: [uniColl_cache, sequence_cache] # ${GP_cache_dir},${GP_HOME}/third-party/data/BacterialPipeline/uniColl/ver-3.2/cache
# type: Directory[]
genemark_path: genemark_path # ${GP_HOME}/third-party/GeneMark
# type: Directory
hmm_params: hmm_params
marked_annotation_name:
default: marked-annotation.asn
min_seq_len:
default: 200
preliminary_models_name: # -out
default: preliminary-models.asn
sequences: raw_seqs
thr: thresholds
tmp_dir_name:
default: workdir
# type: Directory
nogenbank:
default: true
out: [marked_annotation, preliminary_models] # all internal!
Run_GeneMark_Post:
label: "Run GeneMark (genemark_post)"
run: ../progs/genemark_post.cwl
in:
abs_short_model_limit:
default: 60
asn_cache: [uniColl_cache, sequence_cache] # ${GP_cache_dir},${GP_HOME}/third-party/data/BacterialPipeline/uniColl/ver-3.2/cache
# type: Directory[]
genemark_annot: Run_GeneMark/preliminary_models
max_overlap:
default: 120
max_unannotated_region:
default: 5000
models_name: # -out
default: models.asn
out_product_ids_name:
default: all-proteins.ids
product_id_prefix:
default: 'PGAP'
pre_annot: Run_GeneMark/marked_annotation
selenocysteines: selenoproteins
selenocysteines_db: selenocysteines_db
short_model_limit:
default: 180
unicoll_sqlite: naming_sqlite
nogenbank:
default: true
out: [models]
PGAP_plus_ab_initio:
label: "PGAP + ab initio"
run: ../progs/bact_entries_merge.cwl
in:
annotation:
source:
- Run_GeneMark_Post/models
- Good_ab_initio_annotations/out_annotation
linkMerge: merge_flattened
out: [out_annotation]
Extract_Model_Proteins:
label: "Extract Model Proteins"
run: ../progs/protein_extract.cwl
in:
input: PGAP_plus_ab_initio/out_annotation
nogenbank:
default: true
out: [proteins, lds2, seqids]
Search_Naming_HMMs:
label: "Search Naming HMMs"
run: ../task_types/tt_hmmsearch_wnode.cwl
in:
proteins: Extract_Model_Proteins/proteins
hmm_path: naming_hmms_combined # naming_hmms_combined.mft converted to Directory
seqids: Extract_Model_Proteins/seqids
lds2: Extract_Model_Proteins/lds2
hmms_tab: hmms_tab # goes eventually to -fam parameter
asn_cache: sequence_cache
scatter_gather_nchunks: scatter_gather_nchunks
out:
[hmm_hits]
Assign_Naming_HMM_to_Proteins:
label: "Assign Naming HMM to Proteins"
run: ../progs/assign_hmm.cwl
in:
input: Search_Naming_HMMs/hmm_hits
db: naming_sqlite
out: [assignments]
Name_by_WPs:
label: "Name by WPs"
run: ../progs/identify_wp.cwl
in:
wp_hashes: wp_hashes
taxon_db: taxon_db
ifmt:
default: seq-entries
lds2: Extract_Model_Proteins/lds2
proteins: Extract_Model_Proteins/proteins
sequences: PGAP_plus_ab_initio/out_annotation # -input
fast:
default: true
out: [out_names] # -onames, there is also prot2wp, but it goes only to tax check, which we dropped in the first round
outputs:
# long output names are preliminary.
# after the list is complete, drop the long prefixes
Find_Best_Evidence_Alignments_aligns:
# sink: Generate Annotation Reports/cluster_prot_aligns (EXTERNAL, put to output/)
# sink: Validate Annotation/cluster_best_mft (EXTERNAL, put to output/)
label: "goes to protein_alignment/Seed Search Compartments/compartments"
type: File
outputSource: Find_Best_Evidence_Alignments/out_align
Run_GeneMark_Post_models:
type: File
outputSource: Run_GeneMark_Post/models
Extract_Model_Proteins_seqids:
type: File
outputSource: Extract_Model_Proteins/seqids
Extract_Model_Proteins_lds2:
type: File
outputSource: Extract_Model_Proteins/lds2
Extract_Model_Proteins_proteins:
type: File
outputSource: Extract_Model_Proteins/proteins
Search_Naming_HMMs_hmm_hits:
type: File
outputSource: Search_Naming_HMMs/hmm_hits
Assign_Naming_HMM_to_Proteins_assignments:
type: File
outputSource: Assign_Naming_HMM_to_Proteins/assignments
Name_by_WPs_names:
type: File
outputSource: Name_by_WPs/out_names
PGAP_plus_ab_initio_annotation:
type: File
outputSource: PGAP_plus_ab_initio/out_annotation