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taxcheck.cwl
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taxcheck.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
doc: |
Perform taxonomic identification tasks on an input genome
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: LoadListingRequirement
loadListing: deep_listing
inputs:
supplemental_data:
type: Directory
default:
class: Directory
location: input
fasta: File
gc_assm_name:
type: string
default: my_gc_assm_name
report_usage: boolean
submol: File
ignore_all_errors:
type: boolean?
no_internet:
type: boolean?
make_uuid:
type: boolean?
default: true
uuid_in:
type: File?
outputs:
ani_tax_report:
type: File
outputSource: bacterial_kmer/Identify_Top_N_ANI_top
ani_tax_report_text:
type: File
outputSource: bacterial_kmer/Identify_Top_N_ANI_top_txt
errors:
type: File?
outputSource: bacterial_kmer/errors
uuid_out:
type: File
outputSource: ping_start/uuid_out
steps:
ping_start:
run: progs/pinger.cwl
in:
report_usage: report_usage
make_uuid: make_uuid
uuid_in: uuid_in
state:
default: "start"
workflow:
default: "ani-analysis"
instring: gc_assm_name
out: [stdout, outstring, uuid_out]
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]
passdata:
in:
data: supplemental_data
run: expr/ani.cwl
out:
- ANI_cutoff
- ani_report_transform
- gc_cache
- gc_seq_cache
- gcextract2_sqlite
- kmer_cache_sqlite
- kmer_reference_assemblies
- taxon_db
- tax_synon
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]
Prepare_Seq_entries:
run: progs/prepare_seq_entry_input.cwl
in:
entries: prepare_input_template/output_entries
seq_submit: prepare_input_template/output_seq_submit
out: [output_entries]
genomic_source:
run: genomic_source/wf_genomic_source_asn.cwl
in:
entries: prepare_input_template/output_entries
seq_submit: prepare_input_template/output_seq_submit
gc_assm_name: ping_start/outstring
taxon_db: passdata/taxon_db
out: [gencoll_asn, seqid_list, stats_report, asncache, ids_out, submit_block_template]
bacterial_kmer:
run: bacterial_kmer/wf_bacterial_kmer.cwl
in:
Extract_Kmers_From_Input___entry: Prepare_Seq_entries/output_entries
gencoll_asn: genomic_source/gencoll_asn
asn_cache: genomic_source/asncache
gc_seq_cache: passdata/gc_seq_cache
gc_cache: passdata/gc_cache
kmer_cache_sqlite: passdata/kmer_cache_sqlite
ref_assembly_taxid: prepare_input_template/taxid
ref_assembly_id:
default: 0
ANI_cutoff: passdata/ANI_cutoff
kmer_reference_assemblies: passdata/kmer_reference_assemblies
tax_synon: passdata/tax_synon
taxon_db: passdata/taxon_db
gcextract2_sqlite: passdata/gcextract2_sqlite
ani_report_transform: passdata/ani_report_transform
out: [Identify_Top_N_ANI_annot, Identify_Top_N_ANI_top, Extract_Top_Assemblies___tax_report, Identify_Top_N_ANI_top_txt, errors]
ping_stop:
run: progs/pinger.cwl
in:
report_usage: report_usage
uuid_in: ping_start/uuid_out
state:
default: "stop"
workflow:
default: "ani-analysis"
# 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:
- bacterial_kmer/Identify_Top_N_ANI_annot
- bacterial_kmer/Identify_Top_N_ANI_top
- bacterial_kmer/Extract_Top_Assemblies___tax_report
out: [stdout]