/
tt_blastn_wnode.cwl
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tt_blastn_wnode.cwl
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cwlVersion: v1.2
label: "tt_blastn_wnode"
class: Workflow # task type
requirements:
- class: MultipleInputFeatureRequirement
inputs:
asn_cache: Directory
ids_out: File
blastdb_dir: Directory
blastdb: string
evalue: float
word_size: int
max_target_seqs: int?
soft_masking: string?
affinity: string?
max_batch_length: int?
best_hit_overhang: float?
best_hit_score_edge: float?
dust: string?
perc_identity: float?
task: string?
outputs:
blast_align:
type: File
outputSource: gpx_make_outputs/output_file
steps:
gpx_qsubmit:
run: ../progs/gpx_qsubmit.cwl
in:
proteins:
default:
class: File
path: '/dev/null'
basename: 'null'
contents: ''
affinity: affinity
asn_cache:
source: [asn_cache]
linkMerge: merge_flattened
max_batch_length: max_batch_length
ids:
source: [ids_out]
linkMerge: merge_flattened
blastdb_dir: blastdb_dir
blastdb:
source: [blastdb]
linkMerge: merge_flattened
nogenbank:
default: true
out: [jobs]
blastn_wnode:
run: ../progs/blastn_wnode.cwl
in:
asn_cache: asn_cache
evalue: evalue
max_target_seqs: max_target_seqs
soft_masking:
default: 'true'
swap_rows:
default: false
task:
default: blastn
word_size: word_size
input_jobs: gpx_qsubmit/jobs
blastdb_dir: blastdb_dir
blastdb: blastdb
best_hit_overhang: best_hit_overhang
best_hit_score_edge: best_hit_score_edge
dust: dust
perc_identity: perc_identity
out: [outdir]
gpx_make_outputs:
run: ../progs/gpx_make_outputs.cwl
in:
input_path: blastn_wnode/outdir
num_partitions:
default: 1
output:
default: "blast.#.asn"
output_glob:
default: "blast.*.asn"
out: [output_file]