#!/usr/bin/env cwl-runner
label: "PGAP Pipeline"
cwlVersion: v1.0
class: Workflow
doc: PGAP pipeline for external usage, powered via containers
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
#
# User specific input
#
entries: File?
seq_submit: File?
taxid: int
gc_assm_name: string
locus_tag_prefix: string?
dbname: string?
report_usage: boolean
#
# User independent, static input
#
blast_rules_db:
type: string
default: blast_rules_db
scatter_gather_nchunks:
type: string
default: '1'
supplemental_data:
type: Directory
default:
class: Directory
location: input
steps:
ping_start:
run: progs/pinger.cwl
in:
report_usage: report_usage
make_uuid:
default: true
state:
default: "start"
workflow:
default: "pgap"
instring: gc_assm_name
out: [stdout, outstring, uuid_out]
passdata:
in:
data: supplemental_data
run:
class: ExpressionTool
requirements:
InlineJavascriptRequirement: {}
inputs:
data:
type: Directory
expression: |
${
var r = {};
var l = inputs.data.listing;
var n = l.length;
for (var i = 0; i < n; i++) {
switch (l[i].basename) {
case '16S_rRNA':
r['16s_blastdb_dir'] = l[i];
break;
case '23S_rRNA':
r['23s_blastdb_dir'] = l[i];
break;
case 'RF00001.cm':
r['5s_model_path'] = l[i];
break;
case 'AntiFamLib':
r['AntiFamLib'] = l[i];
break;
case 'asn2pas.xsl':
r['asn2pas_xsl'] = l[i];
break;
case 'CDD':
r['CDDdata'] = l[i];
break;
case 'cdd_add':
r['CDDdata2'] = l[i];
break;
case 'product_rules.prt':
r['defline_cleanup_rules'] = l[i];
break;
case 'gene_master.ini':
r['gene_master_ini'] = l[i];
break;
case 'GeneMark':
r['genemark_path'] = l[i];
break;
case 'rfam-amendments.xml':
r['rfam_amendments'] = l[i];
break;
case 'Rfam.selected1.cm':
r['rfam_model_path'] = l[i];
break;
case 'Rfam.seed':
r['rfam_stockholm'] = l[i];
break;
case 'selenoproteins':
r['selenoproteins'] = l[i];
break;
case 'thresholds.xml':
r['thresholds'] = l[i];
break;
case 'uniColl_path':
var ul = l[i].listing;
var un = ul.length;
for (var j = 0; j < un; j++) {
switch (ul[j].basename) {
case 'blast_dir':
r['blast_rules_db_dir'] = ul[j];
r['naming_blast_db'] = ul[j];
break;
case 'real_hmms':
r['hmm_path'] = ul[j];
break;
case 'real_hmms.tab':
r['hmms_tab'] = ul[j];
break;
case 'naming_hmms':
r['naming_hmms_combined'] = ul[j];
break;
case 'naming_hmms.tab':
r['naming_hmms_tab'] = ul[j];
break;
case 'naming.sqlite':
r['naming_sqlite'] = ul[j];
break;
case 'taxonomy.sqlite3':
r['taxon_db'] = ul[j];
break;
case 'cache':
r['uniColl_cache'] = ul[j];
break;
case 'universal.xml':
r['univ_prot_xml'] = ul[j];
break;
case 'wp-hashes.sqlite':
r['wp_hashes'] = ul[j];
break;
}
}
break;
case 'validation-results.xml':
r['val_res_den_xml'] = l[i];
break;
}
}
return r;
}
outputs:
16s_blastdb_dir:
type: Directory
23s_blastdb_dir:
type: Directory
5s_model_path:
type: File
AntiFamLib:
type: Directory
asn2pas_xsl:
type: File
blast_rules_db_dir:
type: Directory
CDDdata:
# ${GP_HOME}/third-party/data/CDD/cdd - this is rpsblastdb
type: Directory
CDDdata2:
# ${GP_HOME}/third-party/data/cdd_add
type: Directory
defline_cleanup_rules:
# defline_cleanup_rules # ${GP_HOME}/etc/product_rules.prt
type: File
gene_master_ini:
type: File
genemark_path:
type: Directory
hmm_path:
type: Directory
hmms_tab:
type: File
naming_blast_db: # NamingDatabase
type: Directory
naming_hmms_combined:
# ${GP_HOME}/third-party/data/BacterialPipeline/uniColl/ver-3.2/naming_hmms_combined.mft
type: Directory
naming_hmms_tab:
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
rfam_amendments:
type: File
rfam_model_path:
type: File
rfam_stockholm:
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, it's blastdb
type: Directory
taxon_db:
type: File
thresholds:
type: File
uniColl_cache:
type: Directory
univ_prot_xml:
type: File
val_res_den_xml:
type: File
wp_hashes:
type: File
out:
- 16s_blastdb_dir
- 23s_blastdb_dir
- 5s_model_path
- AntiFamLib
- asn2pas_xsl
- blast_rules_db_dir
- CDDdata2
- CDDdata
- defline_cleanup_rules
- gene_master_ini
- genemark_path
- hmm_path
- hmms_tab
- naming_blast_db
- naming_hmms_combined
- naming_hmms_tab
- naming_sqlite
- rfam_amendments
- rfam_model_path
- rfam_stockholm
- selenoproteins
- taxon_db
- thresholds
- uniColl_cache
- univ_prot_xml
- val_res_den_xml
- wp_hashes
genomic_source: # PLANE
run: genomic_source/wf_genomic_source_asn.cwl
in:
entries: entries
seq_submit: seq_submit
# taxid: taxid
gc_assm_name: ping_start/outstring
taxon_db: passdata/taxon_db
out: [gencoll_asn, seqid_list, stats_report, asncache, ids_out, submit_block_template]
#
# Pseudo plane "default 1"
#
Prepare_Unannotated_Sequences: # ORIGINAL TASK NAME: Prepare Unannotated Sequences # default 1
label: "Prepare Unannotated Sequences"
run: bacterial_prepare_unannotated.cwl
in:
asn_cache: genomic_source/asncache
gc_assembly: genomic_source/gencoll_asn
ids: genomic_source/seqid_list
submit_block: genomic_source/submit_block_template
taxon_db: passdata/taxon_db
out: [master_desc, sequences]
Cache_Entrez_Gene: # ORIGINAL TASK NAME: Cache Entrez Gene # default 1
label: "Cache Entrez Gene"
run: cache_entrez_gene.cwl
in:
asn_cache: [genomic_source/asncache, passdata/uniColl_cache]
egene_ini: passdata/gene_master_ini
input: Prepare_Unannotated_Sequences/sequences
out: [prok_entrez_gene_stuff]
Create_Genomic_BLASTdb: # default 1
label: "Create Genomic BLASTdb" # default 1
run: progs/gp_makeblastdb.cwl
in:
ids: genomic_source/ids_out
title:
default: 'BLASTdb created by GPipe'
asn_cache:
source: [ genomic_source/asncache ]
linkMerge: merge_flattened
dbtype:
default: 'nucl'
out: [blastdb]
#
# end of pseudo plane "default 1"
#
bacterial_ncrna: # PLANE
run: bacterial_ncrna/wf_gcmsearch.cwl
in:
asn_cache: genomic_source/asncache
seqids: genomic_source/seqid_list
model_path: passdata/rfam_model_path
rfam_amendments: passdata/rfam_amendments
rfam_stockholm: passdata/rfam_stockholm
taxon_db: passdata/taxon_db
out: [annots]
bacterial_mobile_elem: # PLANE
run: bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl
in:
asn_cache: genomic_source/asncache
seqids: genomic_source/seqid_list
out: [annots]
bacterial_noncoding: # PLANE
run: bacterial_noncoding/wf_bacterial_noncoding.cwl
in:
asn_cache: genomic_source/asncache
seqids: genomic_source/seqid_list
16s_blastdb_dir: passdata/16s_blastdb_dir
23s_blastdb_dir: passdata/23s_blastdb_dir
model_path: passdata/5s_model_path
rfam_amendments: passdata/rfam_amendments
rfam_stockholm: passdata/rfam_stockholm
taxon_db: passdata/taxon_db
out: [ annotations_5s, annotations_16s, annotations_23s ]
bacterial_trna: # PLANE
run: bacterial_trna/wf_trnascan.cwl
in:
asn_cache: genomic_source/asncache
seqids: genomic_source/seqid_list
taxid: taxid
taxon_db: passdata/taxon_db
scatter_gather_nchunks: scatter_gather_nchunks
out: [annots]
bacterial_annot: # PLANE
run: bacterial_annot/wf_bacterial_annot_pass1.cwl
in:
asn_cache: genomic_source/asncache
inseq: Prepare_Unannotated_Sequences/sequences
hmm_path: passdata/hmm_path
hmms_tab: passdata/hmms_tab
scatter_gather_nchunks: scatter_gather_nchunks
uniColl_cache: passdata/uniColl_cache
trna_annots: bacterial_trna/annots
ncrna_annots: bacterial_ncrna/annots
nogenbank:
default: true
Execute_CRISPRs_annots: bacterial_mobile_elem/annots
Generate_16S_rRNA_Annotation_annotation: bacterial_noncoding/annotations_16s
Generate_23S_rRNA_Annotation_annotation: bacterial_noncoding/annotations_23s
Post_process_CMsearch_annotations_annots_5S: bacterial_noncoding/annotations_5s
genemark_path: passdata/genemark_path
thresholds: passdata/thresholds
out: [lds2,seqids,proteins, aligns, annotation, out_hmm_params, outseqs, prot_ids]
spurious_annot_1: # PLANE
run: spurious_annot/wf_spurious_annot_pass1.cwl
in:
Extract_ORF_Proteins_proteins: bacterial_annot/proteins
Extract_ORF_Proteins_seqids: bacterial_annot/seqids
Extract_ORF_Proteins_lds2: bacterial_annot/lds2
AntiFamLib: passdata/AntiFamLib
sequence_cache: genomic_source/asncache
scatter_gather_nchunks: scatter_gather_nchunks
out: [AntiFam_tainted_proteins_I___oseqids]
bacterial_annot_2: # PLANE
run: bacterial_annot/wf_bacterial_annot_pass2.cwl
in:
lds2: bacterial_annot/lds2
proteins: bacterial_annot/proteins
prot_ids_A: bacterial_annot/seqids
prot_ids_B1: bacterial_annot/prot_ids
prot_ids_B2: spurious_annot_1/AntiFam_tainted_proteins_I___oseqids
blast_rules_db_dir: passdata/blast_rules_db_dir
blast_rules_db: blast_rules_db
identification_db_dir: passdata/naming_blast_db
annotation: bacterial_annot/outseqs
sequence_cache: genomic_source/asncache
unicoll_cache: passdata/uniColl_cache
scatter_gather_nchunks: scatter_gather_nchunks
out: [aligns] # label: "goes to protein_alignment/Seed Search Compartments/compartments"
protein_alignment: # PLANE
run: protein_alignment/wf_protein_alignment.cwl
in:
asn_cache: genomic_source/asncache
uniColl_asn_cache: passdata/uniColl_cache
naming_sqlite: passdata/naming_sqlite
blastdb_dir: Create_Genomic_BLASTdb/blastdb
taxid: taxid
tax_sql_file: passdata/taxon_db
gc_assembly: genomic_source/gencoll_asn
compartments: bacterial_annot_2/aligns
out: [universal_clusters, align, align_non_match]
bacterial_annot_3:
run: bacterial_annot/wf_bacterial_annot_pass3.cwl
in:
uniColl_cache: passdata/uniColl_cache
sequence_cache: genomic_source/asncache
hmm_aligns: bacterial_annot/aligns
scatter_gather_nchunks: scatter_gather_nchunks
prot_aligns: protein_alignment/align # label: "Filter Protein Alignments I/align"
annotation: bacterial_annot/annotation
raw_seqs: Prepare_Unannotated_Sequences/sequences
thresholds: passdata/thresholds
naming_sqlite: passdata/naming_sqlite
hmm_params: bacterial_annot/out_hmm_params # Run GeneMark Training/hmm_params (EXTERNAL, put to input/
selenoproteins: passdata/selenoproteins
naming_hmms_combined: passdata/naming_hmms_combined
hmms_tab: passdata/naming_hmms_tab
wp_hashes: passdata/wp_hashes
taxon_db: passdata/taxon_db
genemark_path: passdata/genemark_path
out:
- id: Find_Best_Evidence_Alignments_aligns
- id: Run_GeneMark_Post_models
- id: Extract_Model_Proteins_seqids
- id: Extract_Model_Proteins_lds2
- id: Extract_Model_Proteins_proteins
- id: Search_Naming_HMMs_hmm_hits
- id: Assign_Naming_HMM_to_Proteins_assignments
- id: Name_by_WPs_names
spurious_annot_2:
run: spurious_annot/wf_spurious_annot_pass2.cwl
in:
Extract_Model_Proteins_proteins: bacterial_annot_3/Extract_Model_Proteins_proteins
Extract_Model_Proteins_seqids: bacterial_annot_3/Extract_Model_Proteins_seqids
Extract_Model_Proteins_lds2: bacterial_annot_3/Extract_Model_Proteins_lds2
AntiFamLib: passdata/AntiFamLib
sequence_cache: genomic_source/asncache
scatter_gather_nchunks: scatter_gather_nchunks
Run_GeneMark_models: bacterial_annot_3/Run_GeneMark_Post_models
out:
- AntiFam_tainted_proteins___oseqids
- Good_AntiFam_filtered_annotations_out
- Good_AntiFam_filtered_proteins_output
bacterial_annot_4:
run: bacterial_annot/wf_bacterial_annot_pass4.cwl
in:
lds2: bacterial_annot_3/Extract_Model_Proteins_lds2
proteins: bacterial_annot_3/Extract_Model_Proteins_proteins
annotation: spurious_annot_2/Good_AntiFam_filtered_annotations_out
Good_AntiFam_filtered_proteins_gilist: spurious_annot_2/Good_AntiFam_filtered_proteins_output
sequence_cache: genomic_source/asncache
uniColl_cache: passdata/uniColl_cache
naming_blast_db: passdata/naming_blast_db
naming_sqlite: passdata/naming_sqlite
hmm_assignments: bacterial_annot_3/Assign_Naming_HMM_to_Proteins_assignments
wp_assignments: bacterial_annot_3/Name_by_WPs_names
Extract_Model_Proteins_prot_ids: bacterial_annot_3/Extract_Model_Proteins_seqids
CDDdata: passdata/CDDdata
CDDdata2: passdata/CDDdata2
thresholds: passdata/thresholds
defline_cleanup_rules: passdata/defline_cleanup_rules
blast_rules_db_dir: passdata/blast_rules_db_dir
blast_rules_db: blast_rules_db
identification_db_dir: passdata/naming_blast_db
scatter_gather_nchunks: scatter_gather_nchunks
out:
- id: out_annotation
# #
# # Pseudo plane default 2, we do not need that for new submissions in off-NCBI environment
# #
# # Preserve_Annotations: # Pseudo plane default 2
# # run: task_types/tt_preserve_annot.cwl
# # in:
# # asn_cache:
# # source: [genomic_source/asncache]
# # linkMerge: merge_flattened
# # input_annotation: bacterial_annot/annotation
# # rfam_amendments: rfam_amendments
# # no_ncRNA:
# # default: true
# # out: [annotations]
# # preserve_annot_markup: # Pseudo plane default 2
# # # uncharted territory!!!
# # run: preserve_annot_markup.cwl # Preserve Product Accessions
# # in:
# # #seq_cache: genobacterial_prepare_unannotated/asncache
# # #unicoll_cache: uniColl_cache
# # input_annotation: Preserve_Annotations/annotations
# # asn_cache: [genomic_source/asncache, uniColl_cache]
# # egene_ini: gene_master_ini
# # gc_assembly: genomic_source/gencoll_asn
# # input: Preserve_Annotations/annotations
# # prok_entrez_gene_stuff: Cache_Entrez_Gene/prok_entrez_gene_stuff
# # out: [annotations]
# #
# # End of Pseudo plane default 2
# #
# # This step takes input from bacterial_annot 4/Bacterial Annot Filter, see GP-23942
# # Status:
# # tasktype coded, input/output matches
# # application not coded
# ###############################################
# # AMR plane is for later stages skipping
# ###############################################
Add_Locus_Tags:
run: progs/add_locus_tags.cwl
in:
input: bacterial_annot_4/out_annotation
locus_tag_prefix: locus_tag_prefix
dbname: dbname
out: [output]
#
# Pseudo plane default 3
#
#
# Final_Bacterial_Package task
#
Final_Bacterial_Package_asn_cleanup:
run: progs/asn_cleanup.cwl
in:
inp_annotation: Add_Locus_Tags/output # production
serial:
default: binary
out: [annotation]
Final_Bacterial_Package_final_bact_asn:
run: progs/final_bact_asn.cwl
in:
annotation:
source: [Final_Bacterial_Package_asn_cleanup/annotation]
linkMerge: merge_flattened
asn_cache: genomic_source/asncache
gc_assembly: genomic_source/gencoll_asn # gc_create_from_sequences
master_desc: Prepare_Unannotated_Sequences/master_desc
submit_block_template:
source: [genomic_source/submit_block_template]
linkMerge: merge_flattened
it:
default: true
submission_mode_genbank:
default: true
nogenbank:
default: true
out: [outfull]
Final_Bacterial_Package_dumb_down_as_required:
run: progs/dumb_down_as_required.cwl
in:
annotation: Final_Bacterial_Package_final_bact_asn/outfull
asn_cache:
source: [genomic_source/asncache]
linkMerge: merge_flattened
max_x_ratio:
default: 0.1
max_x_run:
default: 3
partial_cov_threshold:
default: 65
partial_len_threshold:
default: 30
drop_partial_in_the_middle:
default: true
submission_mode_genbank:
default: true
nogenbank:
default: true
it:
default: true
out: [outent]
Final_Bacterial_Package_ent2sqn:
run: progs/ent2sqn.cwl
in:
annotation: Final_Bacterial_Package_dumb_down_as_required/outent
asn_cache:
source: [genomic_source/asncache]
linkMerge: merge_flattened
gc_assembly: genomic_source/gencoll_asn # gc_create_from_sequences
submit_block_template:
source: [genomic_source/submit_block_template]
linkMerge: merge_flattened
it:
default: true
out: [output]
Final_Bacterial_Package_sqn2gbent:
run: progs/sqn2gbent.cwl
in:
input: Final_Bacterial_Package_ent2sqn/output
it:
default: true
out: [output]
Generate_Annotation_Reports_gff:
run: progs/gp_annot_format.cwl
in:
input: Final_Bacterial_Package_dumb_down_as_required/outent
ifmt:
default: seq-entry
t:
default: true
ofmt:
default: gff3
exclude_external:
default: true
out: [output]
Generate_Annotation_Reports_gbk:
run: progs/asn2flat.cwl
in:
input: Final_Bacterial_Package_sqn2gbent/output
no_external:
default: true
type:
default: seq-entry
mode:
default: entrez
style:
default: master
gbload:
default: true
out: [output]
Generate_Annotation_Reports_nuc_fasta:
run: progs/asn2fasta.cwl
in:
i: Final_Bacterial_Package_sqn2gbent/output
type:
default: seq-entry
nuc_fasta_name:
default: annot.fna
out: [nuc_fasta]
Generate_Annotation_Reports_prot_fasta:
run: progs/asn2fasta.cwl
in:
i: Final_Bacterial_Package_sqn2gbent/output
type:
default: seq-entry
prot_fasta_name:
default: annot.faa
out: [prot_fasta]
Final_Bacterial_Package_std_validation:
run: progs/std_validation.cwl
in:
annotation: Final_Bacterial_Package_dumb_down_as_required/outent
asn_cache:
source: [genomic_source/asncache]
exclude_asndisc_codes: #
default: ['OVERLAPPING_CDS']
inent: Final_Bacterial_Package_dumb_down_as_required/outent
ingb: Final_Bacterial_Package_sqn2gbent/output
insqn: Final_Bacterial_Package_ent2sqn/output
master_desc:
source: [Prepare_Unannotated_Sequences/master_desc]
linkMerge: merge_flattened
submit_block_template:
source: [genomic_source/submit_block_template]
linkMerge: merge_flattened
it:
default: true
submission_mode_genbank:
default: true
nogenbank:
default: true
out:
- id: outdisc
- id: outdiscxml
- id: outmetamaster
- id: outval
Final_Bacterial_Package_val_stats: # TESTED (unit test)
run: progs/val_stats.cwl
in:
annot_val: Final_Bacterial_Package_std_validation/outval
c_toolkit:
default: true
out: [output, xml]
#
# end of Final_Bacterial_Package task
#
#### we do not need this
# Prepare_Init_Refseq_Molecules:
# run: progs/
#
# Validate_Annotation task
#
Validate_Annotation_bact_univ_prot_stats:
run: progs/bact_univ_prot_stats.cwl
in:
annot_request_id:
default: -1 # this is dummy annot_request_id
hmm_search: bacterial_annot_3/Search_Naming_HMMs_hmm_hits
hmm_search_proteins: bacterial_annot_3/Run_GeneMark_Post_models
input: Final_Bacterial_Package_final_bact_asn/outfull
univ_prot_xml: passdata/univ_prot_xml
val_res_den_xml: passdata/val_res_den_xml
it:
default: true
out: [bact_univ_prot_stats_old_xml, var_bact_univ_prot_details_xml, var_bact_univ_prot_stats_xml]
Validate_Annotation_proc_annot_stats:
run: progs/proc_annot_stats.cwl
in:
input: Final_Bacterial_Package_dumb_down_as_required/outent
max_unannotated_region:
default: 5000
univ_prot_xml: passdata/univ_prot_xml
val_res_den_xml: passdata/val_res_den_xml
it:
default: true
out:
- id: var_proc_annot_stats_xml
- id: var_proc_annot_details_xml
Validate_Annotation_xsltproc_asnvalidate:
run: progs/xsltproc.cwl
in:
xml: Final_Bacterial_Package_val_stats/xml
xslt: passdata/asn2pas_xsl
output_name:
default: 'var_proc_annot_stats.val.xml'
out: [output]
Validate_Annotation_xsltproc_asndisc:
run: progs/xsltproc.cwl
in:
xml: Final_Bacterial_Package_std_validation/outdiscxml
xslt: passdata/asn2pas_xsl
output_name:
default: 'var_proc_annot_stats.disc.xml'
out: [output]
Validate_Annotation_collect_annot_stats: # TESTED (unit test)
run: progs/collect_annot_stats.cwl
in:
input:
source:
- Validate_Annotation_bact_univ_prot_stats/var_bact_univ_prot_stats_xml
- Validate_Annotation_proc_annot_stats/var_proc_annot_stats_xml
- Validate_Annotation_xsltproc_asndisc/output
- Validate_Annotation_xsltproc_asnvalidate/output
linkMerge: merge_flattened
output_name:
default: proc_annot_stats.xml
out: [output]
Validate_Annotation_collect_annot_details:
run: progs/collect_annot_stats.cwl
in:
input:
source:
- Validate_Annotation_bact_univ_prot_stats/var_bact_univ_prot_details_xml
- Validate_Annotation_proc_annot_stats/var_proc_annot_details_xml
linkMerge: merge_flattened
output_name:
default: proc_annot_details.xml
out: [output]
ping_stop:
run: progs/pinger.cwl
in:
report_usage: report_usage
uuid_in: ping_start/uuid_out
state:
default: "stop"
workflow:
default: "pgap"
# Note: the input on the following line should be the same as all of the outputs
# for this workflow, so we ensure this is the final step.
infile:
- Final_Bacterial_Package_sqn2gbent/output
- Generate_Annotation_Reports_gff/output
- Generate_Annotation_Reports_gbk/output
- Generate_Annotation_Reports_nuc_fasta/nuc_fasta
- Generate_Annotation_Reports_prot_fasta/prot_fasta
out: [stdout]
#
# end of Validate_Annotation task
#
#
# End of Pseudo plane default 3
#
###############################################
# taxonomy plane is for later stages skipping
###############################################
#
# Pseudo plane default 4
#
# task: Generate Annotation Reports
#
# Generate_Annotation_Reports_pgaap_prepare_review:
# run: progs/pgaap_prepare_review.cwl
# Generate_Annotation_Reports_lds2_indexer:
# run: progs/lds2_indexer.cwl
#
# comparisons only for pre-existing annotation, one of the next phases
#
# # Generate_Annotation_Reports_comparison_format_curr_comparison:
# # run: progs/comparison_format.cwl
# # Generate_Annotation_Reports_comparison_format_prev_comparison:
# # run: progs/comparison_format.cwl
# # Generate_Annotation_Reports_comparison_format_prev_assm_comparison:
# # run: progs/comparison_format.cwl
# # Generate_Annotation_Reports_comparison_format_ref_comparison:
# # run: progs/comparison_format.cwl
# Generate_Annotation_Reports_bact_asn_stats:
# run: progs/bact_asn_stats.cwl
# in:
# input_annotation: Final_Bacterial_Package_dumb_down_as_required/outent
# it:
# default: true
# out: [output, xml_output]
# Generate_Annotation_Reports_val_format:
# run: progs/val_format.cwl
# Generate_Annotation_Reports_gbproject:
# run: progs/gbproject.cwl
# Generate_Annotation_Reports_asn2nucleotide_fasta:
# run: progs/asn2fasta.cwl
# Generate_Annotation_Reports_asn2all_protein_fasta:
# run: progs/asn2fasta.cwl
# Generate_Annotation_Reports_asn2protein_fasta:
# run: progs/asn2fasta.cwl
# Generate_Annotation_Reports_asn2flat:
# run: progs/asn2flat.cwl
# Generate_Annotation_Reports_format_rrnas:
# run: progs/format_rrnas.cwl
# Generate_Annotation_Reports_asn2rrna_fa:
# run: progs/asn2fasta.cwl
# Generate_Annotation_Reports_gp_annot_format:
# run: progs/gp_annot_format.cwl
# end of task: Generate Annotation Reports
#
#
# End of Pseudo plane default 4
#
outputs:
gbent:
type: File
outputSource: Final_Bacterial_Package_sqn2gbent/output
gff:
type: File
outputSource: Generate_Annotation_Reports_gff/output
gbk:
type: File
outputSource: Generate_Annotation_Reports_gbk/output
nucleotide_fasta:
type: File?
outputSource: Generate_Annotation_Reports_nuc_fasta/nuc_fasta
protein_fasta:
type: File?
outputSource: Generate_Annotation_Reports_prot_fasta/prot_fasta
sqn:
type: File?
outputSource: Final_Bacterial_Package_ent2sqn/output