#!/usr/bin/env cwltool class: Workflow cwlVersion: v1.0 id: _v_i_r_t_u_s_p_e doc: VIRTUS v2.0 label: VIRTUS.PE $namespaces: sbg: 'https://www.sevenbridges.com/' inputs: - id: fastq2 type: File 'sbg:x': -438 'sbg:y': -427 - id: fastq1 type: File 'sbg:x': -445.51458740234375 'sbg:y': -274.6721496582031 - id: genomeDir_human type: Directory 'sbg:x': -305 'sbg:y': -602 - id: outFileNamePrefix_human type: string? 'sbg:x': -304 'sbg:y': -750 - id: nthreads type: int? 'sbg:x': -386.4197082519531 'sbg:y': 242.87530517578125 - id: genomeDir_virus type: Directory 'sbg:x': 417.4296875 'sbg:y': 452.7935791015625 - id: kz_threshold type: float? doc: 'default : 0.1' 'sbg:x': -296.2785949707031 'sbg:y': 411.1441650390625 - id: filename_output type: string? doc: 'default : VIRTUS.output.tsv' 'sbg:x': 886.1015625 'sbg:y': -546 outputs: - id: Log.out_human outputSource: - star_mapping_pe_human/Log.out type: File? 'sbg:x': 201 'sbg:y': -114 - id: Log.progress.out_human outputSource: - star_mapping_pe_human/Log.progress.out type: File? 'sbg:x': 203 'sbg:y': -268 - id: SJ.out.tab_human outputSource: - star_mapping_pe_human/SJ.out.tab type: File? 'sbg:x': 206 'sbg:y': -521.0446166992188 - id: aligned_bam_human outputSource: - star_mapping_pe_human/aligned type: File 'sbg:x': 190.84915161132812 'sbg:y': 381.26885986328125 - id: output_unmapped outputSource: - samtools_view/output type: File 'sbg:x': 340.177001953125 'sbg:y': 225.9409942626953 - id: output_fq2 outputSource: - bedtools_bamtofastq_pe/output_fq2 type: File? 'sbg:x': 558.2530517578125 'sbg:y': -337.0843505859375 - id: output_fq1 outputSource: - bedtools_bamtofastq_pe/output_fq1 type: File 'sbg:x': 562.6327514648438 'sbg:y': -168 - id: SJ.out.tab_virus outputSource: - star_mapping_pe_virus/SJ.out.tab type: File? 'sbg:x': 954.8983154296875 'sbg:y': -110.67289733886719 - id: Log.progress.out_virus outputSource: - star_mapping_pe_virus/Log.progress.out type: File? 'sbg:x': 959.8370361328125 'sbg:y': 193.0820770263672 - id: Log.out_virus outputSource: - star_mapping_pe_virus/Log.out type: File? 'sbg:x': 960.4492797851562 'sbg:y': 331.1433410644531 - id: aligned_virus outputSource: - star_mapping_pe_virus/aligned type: File 'sbg:x': 862.1668090820312 'sbg:y': 348.64471435546875 - id: mappingstats_virus outputSource: - star_mapping_pe_virus/mappingstats type: File? 'sbg:x': 956.122802734375 'sbg:y': 39.143333435058594 - id: mappingstats_human outputSource: - star_mapping_pe_human/mappingstats type: File? 'sbg:x': 206.1626434326172 'sbg:y': -394.3936767578125 - id: aligned_bam_virus_filtered outputSource: - bam_filter_polyx/output type: File? 'sbg:x': 984 'sbg:y': 707 - id: output_coverage outputSource: - samtools_coverage/output type: File 'sbg:x': 1142.3587646484375 'sbg:y': 520.5 - id: output outputSource: - mk_summary_virus_count/output type: File? 'sbg:x': 1276 'sbg:y': -400 steps: - id: fastp_pe in: - id: fastq1 source: fastq1 - id: fastq2 source: fastq2 - id: threads source: nthreads - id: length default: 40 out: - id: out_fastq1 - id: out_fastq2 run: ../tool/fastp/fastp-pe.cwl 'sbg:x': -271.3704528808594 'sbg:y': -358.8819885253906 - id: star_mapping_pe_human in: - id: fq1 source: fastp_pe/out_fastq1 - id: fq2 source: fastp_pe/out_fastq2 - id: genomeDir source: genomeDir_human - id: nthreads source: nthreads - id: outSAMunmapped default: Within - 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-pe/star_mapping-pe.cwl label: 'STAR mapping: running mapping jobs.' 'sbg:x': -29 'sbg:y': -369 - id: samtools_view in: - id: threads source: nthreads - id: f default: 4 - id: prefix default: human - id: bam source: star_mapping_pe_human/aligned out: - id: output run: ../tool/samtools/samtools-view.cwl label: samtools-view 'sbg:x': 179.7147216796875 'sbg:y': 53.134429931640625 - id: bedtools_bamtofastq_pe in: - id: input source: samtools_view/output - id: fq default: unmapped_1.fq - id: fq2 default: unmapped_2.fq out: - id: output_fq1 - id: output_fq2 run: ../tool/bedtools/bedtools-bamtofastq-pe.cwl label: bedtools-bamtofastq-pe 'sbg:x': 315.8917236328125 'sbg:y': -33.99026870727539 - id: star_mapping_pe_virus in: - id: fq1 source: fastq_pair/fq1_paired - id: fq2 source: fastq_pair/fq2_paired - 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-pe/star_mapping-pe.cwl label: 'STAR mapping: running mapping jobs.' 'sbg:x': 753.9961547851562 'sbg:y': 133.0281219482422 - id: bam_filter_polyx in: - id: input source: star_mapping_pe_virus/aligned out: - id: output run: ../tool/samtools/bam_filter_polyx.cwl label: bam_filter_polyX 'sbg:x': 825.17626953125 'sbg:y': 513.4646606445312 - id: kz_filter_fq2 in: - id: threshold default: 0.1 source: kz_threshold - id: input_fq source: bedtools_bamtofastq_pe/output_fq2 - id: output_fq default: kz_2.fq out: - id: output run: ../tool/kz_filter/kz_filter.cwl label: kz-filter_fq2 'sbg:x': 460.7408752441406 'sbg:y': 27.032846450805664 - id: kz_filter_fq1 in: - id: threshold default: 0.1 source: kz_threshold - id: input_fq source: bedtools_bamtofastq_pe/output_fq1 - id: output_fq default: kz_1.fq out: - id: output run: ../tool/kz_filter/kz_filter.cwl label: kz-filter_fq1 'sbg:x': 458 'sbg:y': 155 - id: fastq_pair in: - id: fq1 source: kz_filter_fq1/output - id: fq2 source: kz_filter_fq2/output out: - id: fq1_paired - id: fq2_paired run: ../tool/fastq_pair/fastq_pair.cwl label: fastq_pair 'sbg:x': 577.2360229492188 'sbg:y': 93.92456817626953 - id: samtools_coverage in: - id: input source: bam_filter_polyx/output out: - id: output run: ../tool/samtools/samtools-coverage.cwl label: samtools-coverage 'sbg:x': 960 'sbg:y': 454 - id: mk_summary_virus_count in: - id: input_STARLog source: star_mapping_pe_human/mappingstats - id: input_virus_cov source: samtools_coverage/output - id: input_layout default: PE - id: filename_output default: VIRTUS.output.tsv source: filename_output out: - id: output run: ../tool/mk_summary_virus_count/mk_summary_virus_count.cwl label: mk_summary_virus_count 'sbg:x': 1087 'sbg:y': -400 requirements: [] 'sbg:license': CC BY-NC 4.0 'sbg:links': - id: 'https://github.com/yyoshiaki/VIRTUS2' label: '' 'sbg:toolAuthor': Yoshiaki Yasumizu