/
transcriptome_assemble.cwl
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transcriptome_assemble.cwl
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class: Workflow
cwlVersion: v1.0
id: transcriptome_assemble
label: transcriptome_assemble
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: split_spot
type: boolean?
'sbg:exposed': true
- id: split_files
type: boolean?
'sbg:exposed': true
- id: split_3
type: boolean?
'sbg:exposed': true
- id: skip_technical
type: boolean?
'sbg:exposed': true
- id: runid
type: string
'sbg:exposed': true
- id: output_name
type: string
'sbg:exposed': true
- id: url
type: string
'sbg:exposed': true
- id: minimum_protein_length
type: int
'sbg:exposed': true
- id: domtblout
type: string
'sbg:exposed': true
- id: output_1
type: string
'sbg:exposed': true
- id: cpu
type: int
'sbg:x': 131
'sbg:y': -273
- id: out_flag_1
type: string
'sbg:exposed': true
- id: outfmt_flag
type: string
'sbg:exposed': true
- id: max_target_seqs
type: int?
'sbg:exposed': true
- id: db_flag_1
type: string
'sbg:exposed': true
- id: url_1
type: string
'sbg:exposed': true
- id: output_name_1
type: string
'sbg:exposed': true
- id: max_memory
type: string
'sbg:x': 183.18011474609375
'sbg:y': -25.5
- id: seq_type
type: string
'sbg:exposed': true
- id: est_method
type: string
'sbg:exposed': true
- id: output_dir
type: string?
'sbg:exposed': true
- id: seqType
type: string?
'sbg:exposed': true
- id: db_flag
type: string
'sbg:exposed': true
- id: out_flag
type: string
'sbg:exposed': true
outputs:
- id: output2
outputSource:
- for_trinity/output2
type: File
'sbg:x': 455
'sbg:y': -7
- id: output1
outputSource:
- for_trinity/output1
type: File
'sbg:x': 420
'sbg:y': 360
- id: output
outputSource:
- transdecoder/output
type: Directory?
'sbg:x': 921
'sbg:y': 286
- id: out
outputSource:
- extract_transcript_id/out
type: File?
'sbg:x': 1347
'sbg:y': -70
- id: reverse
outputSource:
- fasterq_dump/reverse
type: File?
'sbg:x': -233.8203125
'sbg:y': 74.5
- id: forward
outputSource:
- fasterq_dump/forward
type: File?
'sbg:x': -203.8203125
'sbg:y': 438.5
- id: blast_results
outputSource:
- blastp/blast_results
type: File
'sbg:x': 1613.68310546875
'sbg:y': 403.5
- id: output_2
outputSource:
- aaea/output
type: Directory?
'sbg:x': 849
'sbg:y': 427
- id: trinity_results
outputSource:
- trinity_pe/trinity_results
type: File
'sbg:x': 654.1796875
'sbg:y': 42.5
- id: blastdbcmd_results
outputSource:
- blastdbcmd/blastdbcmd_results
type: File
'sbg:x': 1350.1796875
'sbg:y': 86.5
- id: db_dir
outputSource:
- makeblastdb/db_dir
type: Directory?
'sbg:x': 1183.18017578125
'sbg:y': 318.5
- id: db_dir_1
outputSource:
- makeblastdb_1/db_dir
type: Directory?
'sbg:x': 1392.18017578125
'sbg:y': 672.5
- id: pep
outputSource:
- transdecoder/pep
type: File?
'sbg:x': 903
'sbg:y': 75
steps:
- id: for_trinity
in:
- id: IN1
source: trim_galore/out1
- id: IN2
source: trim_galore/out2
out:
- id: output1
- id: output2
run: ../../tool/for_trinity/for_trinity.cwl
label: for_trinity
'sbg:x': 316
'sbg:y': 176
- id: fasterq_dump
in:
- id: skip_technical
source: skip_technical
- id: split_3
source: split_3
- id: split_files
source: split_files
- id: split_spot
source: split_spot
- id: runid
source: runid
out:
- id: fastqFiles
- id: forward
- id: reverse
run: ../../tool/fasterq-dump/fasterq-dump.cwl
label: 'fasterq-dump: dump .sra format file to generate fastq file'
'sbg:x': -375
'sbg:y': 222
- id: transdecoder
in:
- id: transcripts
source: trinity_pe/trinity_results
- id: minimum_protein_length
source: minimum_protein_length
out:
- id: output
- id: pep
run: ../../tool/TransDecoder/TransDecoder-TransDecoder.LongOrfs/TransDecoder-TransDecoder.LongOrfs.cwl
label: transdecoder
'sbg:x': 803
'sbg:y': 191
- id: wget-Sod_Cu-hmm
in:
- id: output_name
source: output_name
- id: url
source: url
out:
- id: downloaded
- id: stderr
run: ../../tool/wget/wget.cwl
label: 'wget:Sod_Cu.hmm'
'sbg:x': 874
'sbg:y': -66
- id: gzip
in:
- id: file
source: fasterq_dump/reverse
out:
- id: compressed
- id: stderr
run: ../../tool/gzip/gzip.cwl
'sbg:x': -70
'sbg:y': 147
- id: gzip_1
in:
- id: file
source: fasterq_dump/forward
out:
- id: compressed
- id: stderr
run: ../../tool/gzip/gzip.cwl
'sbg:x': -61
'sbg:y': 306
- id: trim_galore
in:
- id: read1
source: gzip_1/compressed
- id: read2
source: gzip/compressed
- id: fastqc
default: true
- id: trim1
default: true
- id: paired
default: true
out:
- id: out1
- id: out2
run: ../../tool/trim_galore/trim_galore-pe/trim_galore-pe.cwl
label: trim_galore
'sbg:x': 122
'sbg:y': 234
- id: hmmsearch
in:
- id: cpu
source: cpu
- id: domtblout
source: domtblout
- id: hmm
source: wget-Sod_Cu-hmm/downloaded
- id: pep
source: transdecoder/pep
out:
- id: output
run: ../../tool/hmmer/hmmer-hmmsearch/hmmer-hmmsearch.cwl
label: hmmsearch
'sbg:x': 1123
'sbg:y': -176
- id: extract_transcript_id
in:
- id: input
source: hmmsearch/output
- id: output
source: output_1
out:
- id: out
run: ../../tool/extract_transcript_id/extract_transcript_id.cwl
label: extract_transcript_id
'sbg:x': 1205
'sbg:y': -61
- id: wget-uniprot-taxonomy_50557-fasta
in:
- id: output_name
default: uniprot-taxonomy_50557.fasta
source: output_name_1
- id: url
default: 'https://www.uniprot.org/uniprot/?query=taxonomy:50557&format=fasta'
source: url_1
out:
- id: downloaded
- id: stderr
run: ../../tool/wget/wget.cwl
label: 'wget:uniprot-taxonomy_50557.fasta'
'sbg:x': 1019
'sbg:y': 623
- id: makeblastdb_1
in:
- id: input_pep
source: wget-uniprot-taxonomy_50557-fasta/downloaded
- id: out
default: uniprot_insect
out:
- id: db_dir
run: ../../tool/blast/blast-makeblastdb/blast-makeblastdb.cwl
label: makeblastdb
'sbg:x': 1245
'sbg:y': 530
- id: blastp
in:
- id: blastdb_dir
source: makeblastdb_1/db_dir
- id: db_flag
source: db_flag_1
- id: num_threads_flag
source: cpu
- id: out_flag
default: uniprot_insect
source: out_flag_1
- id: outfmt_flag
source: outfmt_flag
- id: query_flag
source: blastdbcmd/blastdbcmd_results
- id: max_target_seqs
source: max_target_seqs
out:
- id: blast_results
run: ../../tool/blast/blast-blastp/blast-blastp.cwl
label: BLASTP search.
'sbg:x': 1455
'sbg:y': 404
- id: trinity_pe
in:
- id: cpu
source: cpu
- id: fq1
source: for_trinity/output1
- id: fq2
source: for_trinity/output2
- id: max_memory
source: max_memory
- id: seq_type
source: seq_type
out:
- id: trinity_results
run: ../../tool/Trinity/Trinity-pe/Trinity-pe.cwl
label: Trinity
'sbg:x': 545
'sbg:y': 174
- id: aaea
in:
- id: thread_count
default: true
- id: left
source: for_trinity/output1
- id: right
source: for_trinity/output2
- id: est_method
default: kallisto
source: est_method
- id: kallisto_add_opts
default: true
- id: prep_reference
default: true
- id: output_dir
source: output_dir
- id: seqType
source: seqType
- id: transcripts
source: trinity_pe/trinity_results
- id: cpu
source: cpu
out:
- id: output
run: ../../tool/Trinity/Trinity-aaea/Trinity-aaea.cwl
label: align_and_estimate_abundance.pl
'sbg:x': 668
'sbg:y': 425
- id: makeblastdb
in:
- id: input_pep
source: transdecoder/pep
- id: out
default: trinity_rslt
out:
- id: db_dir
run: ../../tool/blast/blast-makeblastdb/blast-makeblastdb.cwl
label: makeblastdb
'sbg:x': 1029
'sbg:y': 181
- id: blastdbcmd
in:
- id: blastdb_dir
source: makeblastdb/db_dir
- id: db_flag
source: db_flag
- id: entry_batch_flag
source: extract_transcript_id/out
- id: out_flag
source: out_flag
out:
- id: blastdbcmd_results
run: ../../tool/blast/blast-blastdbcmd/blast-blastdbcmd.cwl
label: Blastdbcmd to dump seqs/info.
'sbg:x': 1231
'sbg:y': 161
requirements: []