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pgap.cwl
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pgap.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
doc: |
PGAP pipeline for external usage, powered via containers,
simple user input: (FASTA + yaml only, no template)
label: 'PGAP Pipeline, simple user input, PGAPX-134'
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: LoadListingRequirement
loadListing: deep_listing
- class: NetworkAccess
networkAccess: true
inputs:
supplemental_data:
type: Directory
default:
class: Directory
location: input
blast_hits_cache_data:
type: Directory?
fasta: File
report_usage: boolean
submol: File
ignore_all_errors:
type: boolean?
no_internet:
type: boolean?
make_uuid:
type: boolean?
default: true
uuid_in:
type: File?
xpath_fail_initial_asndisc:
type: string?
xpath_fail_initial_asnvalidate:
type: string?
xpath_fail_final_asndisc:
type: string?
xpath_fail_final_asnvalidate:
type: string?
outputs:
calls:
outputSource: vecscreen/calls
type: File
gbk:
outputSource: standard_pgap/gbk
type: File
gff:
outputSource: standard_pgap/gff
type: File
gff_enhanced:
outputSource: Generate_Annotation_Reports_gff_enhanced/output
type: File
sqn:
outputSource: standard_pgap/sqn
type: File
input_fasta:
outputSource: fasta
type: File
input_submol:
outputSource: submol
type: File
nucleotide_fasta:
outputSource: standard_pgap/nucleotide_fasta
type: File?
protein_fasta:
outputSource: standard_pgap/protein_fasta
type: File?
cds_nucleotide_fasta:
outputSource: standard_pgap/cds_nucleotide_fasta
type: File?
cds_protein_fasta:
outputSource: standard_pgap/cds_protein_fasta
type: File?
initial_asndisc_error_diag:
type: File?
outputSource: standard_pgap/initial_asndisc_error_diag
initial_asnval_error_diag:
type: File?
outputSource: standard_pgap/initial_asnval_error_diag
final_asndisc_error_diag:
type: File?
outputSource: standard_pgap/final_asndisc_error_diag
final_asnval_error_diag:
type: File?
outputSource: standard_pgap/final_asnval_error_diag
checkm_raw:
type: File
outputSource: standard_pgap/checkm_raw
fastaval_errors:
type: File
outputSource: fastaval/out
steps:
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++) {
if (l[i].basename == 'contam_in_prok_blastdb_dir') {
r['contam_in_prok_blastdb_dir'] = l[i];
}
if (l[i].basename == 'adaptor_fasta.fna') {
r['adaptor_fasta'] = l[i];
}
if (l[i].basename == 'uniColl_path') {
var ul = l[i].listing;
var un = ul.length;
for (var j = 0; j < un; j++) {
if (ul[j].basename == 'taxonomy.sqlite3') {
r['taxon_db'] = ul[j];
}
}
}
}
return r;
}
outputs:
taxon_db:
type: File
adaptor_fasta:
type: File
contam_in_prok_blastdb_dir:
type: Directory
out:
- taxon_db
- adaptor_fasta
- contam_in_prok_blastdb_dir
prepare_input_template:
run: prepare_user_input2.cwl
label: Prepare user input
in:
fasta: fasta
submol: submol
taxon_db: passdata/taxon_db
ignore_all_errors: ignore_all_errors
no_internet: no_internet
out: [output_seq_submit, output_entries, locus_tag_prefix, submol_block_json, taxid]
fastaval:
run: progs/fastaval.cwl
in:
in: fasta
check_min_seqlen:
default: 200
check_internal_ns:
default: true
ignore_all_errors: ignore_all_errors
out: [success, out]
vecscreen:
run: vecscreen/vecscreen.cwl
in:
contig_fasta: fasta
adaptor_fasta: passdata/adaptor_fasta
contam_in_prok_blastdb_dir: passdata/contam_in_prok_blastdb_dir
ignore_all_errors: ignore_all_errors
out: [success, calls]
standard_pgap:
label: PGAP Pipeline
in:
go:
- fastaval/success
- vecscreen/success
entries: prepare_input_template/output_entries
seq_submit: prepare_input_template/output_seq_submit
supplemental_data: supplemental_data
gc_assm_name:
source: "#fasta"
valueFrom: $(inputs.gc_assm_name.basename)
locus_tag_prefix: prepare_input_template/locus_tag_prefix
report_usage: report_usage
taxid: prepare_input_template/taxid
submol_block_json: prepare_input_template/submol_block_json
ignore_all_errors: ignore_all_errors
no_internet: no_internet
make_uuid: make_uuid
uuid_in: uuid_in
blast_hits_cache_data: blast_hits_cache_data
xpath_fail_initial_asndisc: xpath_fail_initial_asndisc
xpath_fail_initial_asnvalidate: xpath_fail_initial_asnvalidate
xpath_fail_final_asndisc: xpath_fail_final_asndisc
xpath_fail_final_asnvalidate: xpath_fail_final_asnvalidate
out: [gbent, gbk, gff, nucleotide_fasta, protein_fasta, cds_nucleotide_fasta, cds_protein_fasta, sqn, initial_asndisc_error_diag, initial_asnval_error_diag, final_asndisc_error_diag, final_asnval_error_diag, checkm_raw, checkm_results]
run: wf_common.cwl
Generate_Annotation_Reports_gff_enhanced:
run: progs/produce_enhanced_gff.cwl
in:
gff: standard_pgap/gff
fasta: fasta
out: [output]