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transcriptome_annotation.cwl
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transcriptome_annotation.cwl
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class: Workflow
cwlVersion: v1.0
id: transcriptome_annotation
label: transcriptome_annotation
inputs:
- id: blast_db_dir
type: Directory
- id: fasta
type: File
label: query
- id: evalue
type: float?
- id: blast_nt_db
type: string
- id: threads
type: int?
- id: blast_nr_db
type: string
- id: blast_cdd_db
type: string
outputs:
- id: transdecoder_protein
outputSource:
- transdecoder_longorfs_extract_result/output
type: File
label: Transdecoder-output
- id: blastn_output
outputSource:
- blastn/output
type: File
label: BlastN-output
- id: rpst_blast_output
outputSource:
- rpstblastn/output
type: File
label: RPST-BlastN-output
- id: blastp_output
outputSource:
- blastp/output
type: File
label: BlastP-output
- id: rps_blast_output
outputSource:
- rpsblast/output
type: File
label: RPS-Blast-output
steps:
- id: blastn
in:
- id: db
source: blast_nt_db
- id: dbdir
source: blast_db_dir
- id: evalue
source: evalue
- id: max_target_seqs
default: 1000
- id: num_threads
source: threads
- id: out
valueFrom: '${ return inputs.query.nameroot + "_blastn.tsv";}'
- id: query
source: fasta
out:
- id: export_search_strategy_output
- id: output
run: ../../tools/blast/blastn.cwl
label: BlastN
- id: blastp
in:
- id: db
source: blast_nr_db
- id: dbdir
source: blast_db_dir
- id: evalue
source: evalue
- id: max_target_seqs
default: 1000
- id: num_threads
source: threads
- id: out
valueFrom: '${ return inputs.query.nameroot + "_blastp.tsv";}'
- id: query
source: transdecoder_longorfs_extract_result/output
- id: task
default: blastp-fast
out:
- id: export_search_strategy_output
- id: output
run: ../../tools/blast/blastp.cwl
label: BlastP
- id: rpstblastn
in:
- id: db
source: blast_cdd_db
- id: dbdir
source: blast_db_dir
- id: evalue
source: evalue
- id: max_target_seqs
default: 1000
- id: num_threads
source: threads
- id: out
valueFrom: '${ return inputs.query.nameroot + "_rpstblastn.tsv";}'
- id: query
source: fasta
out:
- id: export_search_strategy_output
- id: output
run: ../../tools/blast/rpstblastn.cwl
label: RPST-BlastN
- id: rpsblast
in:
- id: db
source: blast_cdd_db
- id: dbdir
source: blast_db_dir
- id: evalue
source: evalue
- id: max_target_seqs
default: 1000
- id: num_threads
source: threads
- id: out
valueFrom: '${ return inputs.query.nameroot + "_rpsblast.tsv";}'
- id: query
source: transdecoder_longorfs_extract_result/output
out:
- id: export_search_strategy_output
- id: output
run: ../../tools/blast/rpsblast.cwl
label: RPS-Blast
- id: transdecoder_longorfs
in:
- id: t
source: fasta
out:
- id: output
run: ../../tools/transdecoder/transdecoder_longorfs.cwl
label: TransDecoder
- id: transdecoder_longorfs_extract_result
in:
- id: d
source: transdecoder_longorfs/output
- id: filename
default: longest_orfs.pep
- id: o
valueFrom: '${ return inputs.d.nameroot .replace(".fa", "_transdecoder.fa");}'
out:
- id: output
run: ../../tools/transdecoder/transdecoder_longorfs_extract_result.cwl
label: TransDecoder-Filter
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement