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wf_bacterial_annot_pass4.cwl
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wf_bacterial_annot_pass4.cwl
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#!/usr/bin/env cwl-runner
label: "Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)"
cwlVersion: v1.2
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
scatter_gather_nchunks:
type: string
lds2: # Extract Model Proteins/lds2
type: File
proteins: # Extract Model Proteins/proteins
type: File
annotation: # Good, AntiFam filtered annotations
type: File
Good_AntiFam_filtered_proteins_gilist:
type: File
sequence_cache:
type: Directory
uniColl_cache:
type: Directory
naming_sqlite: # see bacterial_annot_pass3
type: File
hmm_assignments: # XML assignments
type: File
wp_assignments: # XML assignments
type: File
Extract_Model_Proteins_prot_ids: # pass 3
type: File
CDDdata: # ${GP_HOME}/third-party/data/CDD/cdd -
type: Directory
CDDdata2: # ${GP_HOME}/third-party/data/cdd_add
type: Directory
thresholds:
type: File
defline_cleanup_rules: # defline_cleanup_rules # ${GP_HOME}/etc/product_rules.prt
type: File
blast_rules_db:
label: "parameter to store the literal 'blast_rules_db'"
type: string
default: blast_rules_db
blastdb:
label: "Input blastdb databases"
type: string[]
identification_db_dir:
type: Directory
taxid:
type: int
blast_hits_cache:
type: File?
taxon_db:
type: File
genus_list:
type: int[]
steps:
Find_Naming_Protein_Hits:
label: "Find Naming Protein Hits"
run: ../task_types/tt_blastp_wnode_naming.cwl
in:
scatter_gather_nchunks: scatter_gather_nchunks
# files/directories
ids:
source: [Good_AntiFam_filtered_proteins_gilist]
linkMerge: merge_flattened
lds2: lds2
proteins: proteins
blastdb_dir: identification_db_dir
blastdb:
source: #will this fly?
- blastdb # Get_Proteins/selected_blastdb
- blast_rules_db
linkMerge: merge_flattened
# cluster_blastp_wnode_output: cluster_blastp_wnode_output # shortcut
# literal parameters
affinity:
default: subject
asn_cache: [sequence_cache, uniColl_cache]
align_filter:
default: 'score>0 && pct_identity_gapopen_only > 35'
allow_intersection:
default: true
# batch-size:
# default: 1
comp_based_stats:
default: F
compart:
default: true
dbsize:
default: '6000000000'
delay:
default: 0
evalue:
default: 0.1
# extra_coverage: # application default
max_batch_length:
default: 10000
max_jobs:
default: 1
max_target_seqs:
default: 50
no_merge:
default: false
nogenbank:
default: true
ofmt:
default: asn-binary
seg:
default: '30 2.2 2.5'
soft_masking:
default: 'yes'
threshold:
default: 21
top_by_score:
default: 10
word_size:
default: 6
taxid: taxid
genus_list: genus_list
blast_hits_cache:
source: blast_hits_cache
blast_type:
default: 'predicted-protein'
taxon_db: taxon_db
out: [blast_align] # does not go out
Find_best_protein_hits:
label: "Find best protein hits"
run: ../progs/align_filter.cwl
in:
input: Find_Naming_Protein_Hits/blast_align
# input: cached_Find_Naming_Protein_Hits # for shortcuts
asn_cache: [sequence_cache, uniColl_cache]
filter:
default: 'subject_coverage >= 10'
ifmt:
default: seq-align-set
nogenbank:
default: true
out: [o]
Assign_Clusters_to_Proteins_sort:
label: "Assign Clusters to Proteins: pre-sort alignments"
run: ../progs/align_sort.cwl
in:
input: Find_best_protein_hits/o
ifmt:
default: seq-align-set
k:
default: query,subject,-score,-num_ident,query_align_len,subject_align_len,query_start,subject_start
limit_mem:
default: '13G'
nogenbank:
default: true
# internal: tmp
out: [output]
Assign_Clusters_to_Proteins:
label: "Assign Clusters to Proteins: actual task"
run: ../progs/assign_cluster.cwl
in:
asn_cache: [sequence_cache, uniColl_cache]
lds2: lds2
proteins: proteins
comp_based_stats:
default: F
cutoff:
default: 0.5
hfmt:
default: seq-align
hits: Assign_Clusters_to_Proteins_sort/output
margin:
default: 0.05
namedb_dir: identification_db_dir # NamingDatabase
namedb:
default: blast_rules_db
seg:
default: no
sure_cutoff:
default: 0.15
task:
default: blastp
threshold:
default: 21
unicoll_sqlite: naming_sqlite
word_size:
default: 6
nogenbank:
default: true
out: [protein_assignments] # xml format does, not go out of the workflow
Prepare_SPARCLBL_input:
label: "Prepare SPARCLBL input"
run: ../progs/prepare_sparclbl_input.cwl
in:
other_assignments:
source: [Assign_Clusters_to_Proteins/protein_assignments, hmm_assignments, wp_assignments]
linkMerge: merge_flattened
input: Extract_Model_Proteins_prot_ids # pass 3
unicoll_sqlite: naming_sqlite
out: [prot_ids, precedences] # not go out of the workflow
Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences:
label: "Assign SPARCL Architecture Names to Proteins"
run: ../progs/gp_fetch_sequences.cwl
in:
# not sure why do we have this in PGAP.
# asn_cache: [full_id_cache]
# linkMerge: merge_flattened
input: Prepare_SPARCLBL_input/prot_ids
lds2: lds2
proteins: proteins
out: [output]
Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta:
label: "Assign SPARCL Architecture Names to Proteins"
run: ../progs/asn2fasta.cwl
in:
i: Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/output
serial:
default: binary
type:
default: seq-entry
prots_only:
default: true
fasta_name:
default: proteins.fa
out: [fasta]
Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl:
label: "Assign SPARCL Architecture Names to Proteins"
run: ../progs/sparclbl.cwl
in:
s: Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/fasta
p: Prepare_SPARCLBL_input/precedences
m: # number_of_blast_processes
default: 20
n: # max_files_per_proc
default: 500
b: CDDdata
d: CDDdata2
x:
default: 1
out: [protein_assignments] # not go out of the workflow
Add_Names_to_Proteins:
label: "Add Names to Proteins"
run: ../progs/add_prot_names_to_annot.cwl
in:
# let's ditch full_id_cache for now
# asn_cache: [sequence_cache, full_id_cache]
asn_cache:
source: [sequence_cache]
linkMerge: merge_flattened
defline_cleanup_rules: defline_cleanup_rules # ${GP_HOME}/etc/product_rules.prt
proteins:
- Assign_Clusters_to_Proteins/protein_assignments
- Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/protein_assignments
- hmm_assignments
- wp_assignments
input: annotation # Good, AntiFam filtered annotations
unicoll_sqlite: naming_sqlite
nogenbank:
default: true
submission_mode_genbank:
default: true
out: [out_annotation]
Bacterial_Annot_Filter:
label: "Bacterial Annot Filter"
run: ../progs/bact_annot_filter.cwl
in:
abs_short_model_limit:
default: 60
asn_cache:
source: [sequence_cache]
linkMerge: merge_flattened
input:
source: [Add_Names_to_Proteins/out_annotation]
linkMerge: merge_flattened
long_model_limit:
default: 1000000 # 1,000,000
max_overlap:
default: 120
max_unannotated_region:
default: 5000
short_model_limit:
default: 180
thr: thresholds
nogebank:
default: true
out:
- out_annotation # this goes out
# - good_proteins # internal to taxcheck
# this is later.
# WP_Tax_Check:
# label: "WP Tax Check"
# run: ../progs/wp_taxcheck.cwl
# in:
# __input__: Bacterial_Annot_Filter/good_proteins
outputs:
out_annotation:
type: File
outputSource: Bacterial_Annot_Filter/out_annotation