#!/usr/bin/env cwltool
class: Workflow
cwlVersion: v1.0
id: VIRTUS.SE
doc: VIRTUS v1.2.1
label: VIRTUS.SE
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: genomeDir_human
type: Directory
'sbg:x': -305
'sbg:y': -602
- id: outFileNamePrefix_human
type: string?
'sbg:x': -317.6976318359375
'sbg:y': -741.7814331054688
- id: nthreads
type: int?
'sbg:x': -366.3414611816406
'sbg:y': 303.09088134765625
- id: salmon_index_human
type: Directory
'sbg:x': -313.94915771484375
'sbg:y': -922.5796508789062
- id: salmon_quantdir_human
type: string
'sbg:x': -314.884765625
'sbg:y': -1090
- id: fastq
type: File
'sbg:x': -433.9359130859375
'sbg:y': -313.2906188964844
- id: genomeDir_virus
type: Directory
'sbg:x': 447.2225036621094
'sbg:y': -263.0279846191406
- id: hit_cutoff
type: int?
'sbg:x': 738.9225463867188
'sbg:y': 519.65234375
- id: kz_threshold
type: float?
doc: 'default : 0.1'
'sbg:x': -254.75790405273438
'sbg:y': 476.1842956542969
outputs:
- id: output_unmapped
outputSource:
- samtools_view/output
type: File
'sbg:x': 412
'sbg:y': 218
- id: output
outputSource:
- mk_summary_virus_count/output
type: File?
'sbg:x': 1280.2369384765625
'sbg:y': -573.7061767578125
- id: aligned_bam_human
outputSource:
- star_mapping_se/aligned
type: File
'sbg:x': 197.3414306640625
'sbg:y': -108.84769439697266
- id: Log.out_human
outputSource:
- star_mapping_se/Log.out
type: File?
'sbg:x': 276.6431579589844
'sbg:y': -230.89942932128906
- id: mappingstats_human
outputSource:
- star_mapping_se/mappingstats
type: File?
'sbg:x': 262.7428894042969
'sbg:y': -369.5159912109375
- id: SJ.out.tab_human
outputSource:
- star_mapping_se/SJ.out.tab
type: File?
'sbg:x': 240.66200256347656
'sbg:y': -499.92999267578125
- id: output_quantdir_human
outputSource:
- salmon_quant_se/output_quantdir
type: Directory
'sbg:x': 241.95457458496094
'sbg:y': -672.1799926757812
- id: output_fq
outputSource:
- bedtools_bamtofastq_se/output_fq
type: File
'sbg:x': 605.4130859375
'sbg:y': -62.6005744934082
- id: SJ.out.tab_virus
outputSource:
- star_mapping_se_virus/SJ.out.tab
type: File?
'sbg:x': 848.7875366210938
'sbg:y': -104.10987854003906
- id: mappingstats_virus
outputSource:
- star_mapping_se_virus/mappingstats
type: File?
'sbg:x': 889.2903442382812
'sbg:y': 25.706695556640625
- id: Log.out_virus
outputSource:
- star_mapping_se_virus/Log.out
type: File?
'sbg:x': 916.2921752929688
'sbg:y': 166.94712829589844
- id: aligned_bam_virus
outputSource:
- star_mapping_se_virus/aligned
type: File
'sbg:x': 844.6334228515625
'sbg:y': 646.7491455078125
- id: aligned_bam_virus_filtered
outputSource:
- bam_filter_polyx/output
type: File?
'sbg:x': 949.710693359375
'sbg:y': 282.77105712890625
steps:
- id: samtools_view
in:
- id: threads
source: nthreads
- id: f
default: 4
- id: prefix
default: human
- id: bam
source: star_mapping_se/aligned
out:
- id: output
run: ../tool/samtools/samtools-view.cwl
label: samtools-view
'sbg:x': 199.102294921875
'sbg:y': 52.59203338623047
- id: mk_virus_count
in:
- id: virus_bam
source: bam_filter_polyx/output
- id: hit_cutoff
default: 400
source: hit_cutoff
out:
- id: virus_count
run: ../tool/mk_virus_count.cwl
label: mk_virus_count
'sbg:x': 963.22509765625
'sbg:y': 479.8780822753906
- id: mk_summary_virus_count
in:
- id: input_STARLog
source: star_mapping_se/mappingstats
- id: input_virus_count
source: mk_virus_count/virus_count
- id: input_layout
default: SE
out:
- id: output
run: ../tool/mk_summary_virus_count/mk_summary_virus_count.cwl
label: mk_summary_virus_count
'sbg:x': 1132.9288330078125
'sbg:y': -576.298583984375
- id: fastp_se
in:
- id: fastq
source: fastq
- id: threads
source: nthreads
- id: length
default: 40
out:
- id: out_fastq
run: ../tool/fastp/fastp-se.cwl
'sbg:x': -266.3377380371094
'sbg:y': -332.6100769042969
- id: star_mapping_se
in:
- id: fq
source: fastp_se/out_fastq
- id: genomeDir
source: genomeDir_human
- id: nthreads
source: nthreads
- id: outFileNamePrefix
source: outFileNamePrefix_human
- id: outSAMtype
default: BAM SortedByCoordinate
out:
- id: aligned
- id: bamRemDups
- id: mappingstats
- id: readspergene
- id: transcriptomesam
- id: Log.out
- id: Log.progress.out
- id: SJ.out.tab
- id: unmapped
run: ../tool/star/star_mapping-se/star_mapping-se.cwl
label: 'STAR mapping: running mapping jobs.'
'sbg:x': 7.433086395263672
'sbg:y': -424.0473327636719
- id: salmon_quant_se
in:
- id: index
source: salmon_index_human
- id: inf
source: fastp_se/out_fastq
- id: libType
default: A
- id: quantdir
default: salmon_quantdir_human
source: salmon_quantdir_human
- id: runThreadN
source: nthreads
- id: gcBias
default: true
- id: validateMappings
default: true
out:
- id: output_quantdir
run: ../tool/salmon-cwl/salmon-quant_se.cwl
'sbg:x': -10.507709503173828
'sbg:y': -671.244873046875
- id: bedtools_bamtofastq_se
in:
- id: input
source: samtools_view/output
- id: fq
default: unmapped.fq
out:
- id: output_fq
run: ../tool/bedtools/bedtools-bamtofastq-se.cwl
label: bedtools-bamtofastq-pe
'sbg:x': 350.34454345703125
'sbg:y': -113.04795837402344
- id: star_mapping_se_virus
in:
- id: fq
source: kz_filter/output
- id: genomeDir
source: genomeDir_virus
- id: nthreads
source: nthreads
- id: outFileNamePrefix
default: virus
- id: outSAMtype
default: BAM SortedByCoordinate
out:
- id: aligned
- id: bamRemDups
- id: mappingstats
- id: readspergene
- id: transcriptomesam
- id: Log.out
- id: Log.progress.out
- id: SJ.out.tab
- id: unmapped
run: ../tool/star/star_mapping-se/star_mapping-se.cwl
label: 'STAR mapping: running mapping jobs.'
'sbg:x': 722.9669799804688
'sbg:y': 137.9506378173828
- id: bam_filter_polyx
in:
- id: input
source: star_mapping_se_virus/aligned
out:
- id: output
run: ../tool/samtools/bam_filter_polyx.cwl
label: bam_filter_polyX
'sbg:x': 847.6024780273438
'sbg:y': 366.4100036621094
- id: kz_filter
in:
- id: threshold
default: 0.1
source: kz_threshold
- id: input_fq
source: bedtools_bamtofastq_se/output_fq
- id: output_fq
default: kz.fq
out:
- id: output
run: ../tool/kz_filter/kz_filter.cwl
label: kz-filter
'sbg:x': 489.5152893066406
'sbg:y': 39.372711181640625
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
'sbg:license': CC BY-NC 4.0
'sbg:links':
- id: 'https://github.com/yyoshiaki/VIRTUS'
label: ''
'sbg:toolAuthor': Yoshiaki Yasumizu