class: Workflow cwlVersion: v1.0 $namespaces: edam: "http://edamontology.org/" s: "https://schema.org/" inputs: - id: reference_prefix type: string - id: num_threads type: int? - id: SraRunTable type: File - id: url type: string - id: output_name type: string - id: url_1 type: string - id: output_name_1 type: string - id: runThreadN type: string? - id: split_files type: boolean? - id: runid type: string - id: rsem_index_prefix type: string? - id: nthreads type: int? - id: runid_1 type: string - id: runid_2 type: string - id: runid_3 type: string - id: runid_4 type: string - id: runid_5 type: string - id: runid_6 type: string - id: quantMode type: string - id: outSAMtype type: "string[]" - id: nthreads_1 type: int? - id: nthreads_2 type: int? - id: nthreads_3 type: int? - id: nthreads_4 type: int? - id: nthreads_5 type: int? - id: nthreads_6 type: int? outputs: - id: starIndex outputSource: - star_index/starIndex type: Directory - id: rsem_index_1 outputSource: - rsem_index/rsem_index type: Directory - id: downloaded outputSource: - wget/downloaded type: File - id: downloaded_1 outputSource: - wget_1/downloaded type: File - id: transcriptomesam outputSource: - star_rsem_wf_pe/transcriptomesam type: File? - id: transcript_sorted_bam_bai outputSource: - star_rsem_wf_pe/transcript_sorted_bam_bai type: File? - id: transcriptomesam_1 outputSource: - star_rsem_wf_pe_1/transcriptomesam type: File? - id: genes_result outputSource: - star_rsem_wf_pe/genes_result type: File - id: transcript_sorted_bam outputSource: - star_rsem_wf_pe/transcript_sorted_bam type: File? - id: transcript_bam outputSource: - star_rsem_wf_pe/transcript_bam type: File - id: stat outputSource: - star_rsem_wf_pe/stat type: Directory - id: SJ.out.tab outputSource: - star_rsem_wf_pe/SJ.out.tab type: File? - id: readspergene outputSource: - star_rsem_wf_pe/readspergene type: File? - id: mappingstats outputSource: - star_rsem_wf_pe/mappingstats type: File? - id: Log.progress.out outputSource: - star_rsem_wf_pe/Log.progress.out type: File? - id: Log.out outputSource: - star_rsem_wf_pe/Log.out type: File? - id: isoforms_result outputSource: - star_rsem_wf_pe/isoforms_result type: File - id: fastqFiles outputSource: - star_rsem_wf_pe/fastqFiles type: "File[]" - id: bamRemDups outputSource: - star_rsem_wf_pe/bamRemDups type: File? - id: aligned outputSource: - star_rsem_wf_pe/aligned type: File - id: transcript_sorted_bam_bai_1 outputSource: - star_rsem_wf_pe_1/transcript_sorted_bam_bai type: File? - id: transcript_sorted_bam_1 outputSource: - star_rsem_wf_pe_1/transcript_sorted_bam type: File? - id: transcript_bam_1 outputSource: - star_rsem_wf_pe_1/transcript_bam type: File - id: stat_1 outputSource: - star_rsem_wf_pe_1/stat type: Directory - id: SJ.out.tab_1 outputSource: - star_rsem_wf_pe_1/SJ.out.tab type: File? - id: readspergene_1 outputSource: - star_rsem_wf_pe_1/readspergene type: File? - id: mappingstats_1 outputSource: - star_rsem_wf_pe_1/mappingstats type: File? - id: Log.progress.out_1 outputSource: - star_rsem_wf_pe_1/Log.progress.out type: File? - id: Log.out_1 outputSource: - star_rsem_wf_pe_1/Log.out type: File? - id: isoforms_result_1 outputSource: - star_rsem_wf_pe_1/isoforms_result type: File - id: genes_result_1 outputSource: - star_rsem_wf_pe_1/genes_result type: File - id: fastqFiles_1 outputSource: - star_rsem_wf_pe_1/fastqFiles type: "File[]" - id: bamRemDups_1 outputSource: - star_rsem_wf_pe_1/bamRemDups type: File? - id: aligned_1 outputSource: - star_rsem_wf_pe_1/aligned type: File - id: transcriptomesam_2 outputSource: - star_rsem_wf_pe_2/transcriptomesam type: File? - id: transcript_sorted_bam_bai_2 outputSource: - star_rsem_wf_pe_2/transcript_sorted_bam_bai type: File? - id: transcript_sorted_bam_2 outputSource: - star_rsem_wf_pe_2/transcript_sorted_bam type: File? - id: transcript_bam_2 outputSource: - star_rsem_wf_pe_2/transcript_bam type: File - id: stat_2 outputSource: - star_rsem_wf_pe_2/stat type: Directory - id: SJ.out.tab_2 outputSource: - star_rsem_wf_pe_2/SJ.out.tab type: File? - id: readspergene_2 outputSource: - star_rsem_wf_pe_2/readspergene type: File? - id: mappingstats_2 outputSource: - star_rsem_wf_pe_2/mappingstats type: File? - id: Log.progress.out_2 outputSource: - star_rsem_wf_pe_2/Log.progress.out type: File? - id: Log.out_2 outputSource: - star_rsem_wf_pe_2/Log.out type: File? - id: isoforms_result_2 outputSource: - star_rsem_wf_pe_2/isoforms_result type: File - id: genes_result_2 outputSource: - star_rsem_wf_pe_2/genes_result type: File - id: fastqFiles_2 outputSource: - star_rsem_wf_pe_2/fastqFiles type: "File[]" - id: bamRemDups_2 outputSource: - star_rsem_wf_pe_2/bamRemDups type: File? - id: aligned_2 outputSource: - star_rsem_wf_pe_2/aligned type: File - id: transcriptomesam_3 outputSource: - star_rsem_wf_pe_3/transcriptomesam type: File? - id: transcript_sorted_bam_bai_3 outputSource: - star_rsem_wf_pe_3/transcript_sorted_bam_bai type: File? - id: transcript_sorted_bam_3 outputSource: - star_rsem_wf_pe_3/transcript_sorted_bam type: File? - id: transcript_bam_3 outputSource: - star_rsem_wf_pe_3/transcript_bam type: File - id: stat_3 outputSource: - star_rsem_wf_pe_3/stat type: Directory - id: SJ.out.tab_3 outputSource: - star_rsem_wf_pe_3/SJ.out.tab type: File? - id: readspergene_3 outputSource: - star_rsem_wf_pe_3/readspergene type: File? - id: mappingstats_3 outputSource: - star_rsem_wf_pe_3/mappingstats type: File? - id: Log.progress.out_3 outputSource: - star_rsem_wf_pe_3/Log.progress.out type: File? - id: Log.out_3 outputSource: - star_rsem_wf_pe_3/Log.out type: File? - id: isoforms_result_3 outputSource: - star_rsem_wf_pe_3/isoforms_result type: File - id: genes_result_3 outputSource: - star_rsem_wf_pe_3/genes_result type: File - id: fastqFiles_3 outputSource: - star_rsem_wf_pe_3/fastqFiles type: "File[]" - id: bamRemDups_3 outputSource: - star_rsem_wf_pe_3/bamRemDups type: File? - id: aligned_3 outputSource: - star_rsem_wf_pe_3/aligned type: File - id: transcriptomesam_4 outputSource: - star_rsem_wf_pe_4/transcriptomesam type: File? - id: transcript_sorted_bam_bai_4 outputSource: - star_rsem_wf_pe_4/transcript_sorted_bam_bai type: File? - id: transcript_sorted_bam_4 outputSource: - star_rsem_wf_pe_4/transcript_sorted_bam type: File? - id: transcript_bam_4 outputSource: - star_rsem_wf_pe_4/transcript_bam type: File - id: stat_4 outputSource: - star_rsem_wf_pe_4/stat type: Directory - id: SJ.out.tab_4 outputSource: - star_rsem_wf_pe_4/SJ.out.tab type: File? - id: readspergene_4 outputSource: - star_rsem_wf_pe_4/readspergene type: File? - id: mappingstats_4 outputSource: - star_rsem_wf_pe_4/mappingstats type: File? - id: Log.progress.out_4 outputSource: - star_rsem_wf_pe_4/Log.progress.out type: File? - id: Log.out_4 outputSource: - star_rsem_wf_pe_4/Log.out type: File? - id: isoforms_result_4 outputSource: - star_rsem_wf_pe_4/isoforms_result type: File - id: genes_result_4 outputSource: - star_rsem_wf_pe_4/genes_result type: File - id: fastqFiles_4 outputSource: - star_rsem_wf_pe_4/fastqFiles type: "File[]" - id: bamRemDups_4 outputSource: - star_rsem_wf_pe_4/bamRemDups type: File? - id: aligned_4 outputSource: - star_rsem_wf_pe_4/aligned type: File - id: transcriptomesam_5 outputSource: - star_rsem_wf_pe_5/transcriptomesam type: File? - id: transcript_sorted_bam_bai_5 outputSource: - star_rsem_wf_pe_5/transcript_sorted_bam_bai type: File? - id: transcript_sorted_bam_5 outputSource: - star_rsem_wf_pe_5/transcript_sorted_bam type: File? - id: transcript_bam_5 outputSource: - star_rsem_wf_pe_5/transcript_bam type: File - id: stat_5 outputSource: - star_rsem_wf_pe_5/stat type: Directory - id: SJ.out.tab_5 outputSource: - star_rsem_wf_pe_5/SJ.out.tab type: File? - id: readspergene_5 outputSource: - star_rsem_wf_pe_5/readspergene type: File? - id: mappingstats_5 outputSource: - star_rsem_wf_pe_5/mappingstats type: File? - id: Log.progress.out_5 outputSource: - star_rsem_wf_pe_5/Log.progress.out type: File? - id: Log.out_5 outputSource: - star_rsem_wf_pe_5/Log.out type: File? - id: isoforms_result_5 outputSource: - star_rsem_wf_pe_5/isoforms_result type: File - id: genes_result_5 outputSource: - star_rsem_wf_pe_5/genes_result type: File - id: fastqFiles_5 outputSource: - star_rsem_wf_pe_5/fastqFiles type: "File[]" - id: bamRemDups_5 outputSource: - star_rsem_wf_pe_5/bamRemDups type: File? - id: aligned_5 outputSource: - star_rsem_wf_pe_5/aligned type: File - id: transcriptomesam_6 outputSource: - star_rsem_wf_pe_6/transcriptomesam type: File? - id: transcript_sorted_bam_bai_6 outputSource: - star_rsem_wf_pe_6/transcript_sorted_bam_bai type: File? - id: transcript_sorted_bam_6 outputSource: - star_rsem_wf_pe_6/transcript_sorted_bam type: File? - id: transcript_bam_6 outputSource: - star_rsem_wf_pe_6/transcript_bam type: File - id: stat_6 outputSource: - star_rsem_wf_pe_6/stat type: Directory - id: SJ.out.tab_6 outputSource: - star_rsem_wf_pe_6/SJ.out.tab type: File? - id: readspergene_6 outputSource: - star_rsem_wf_pe_6/readspergene type: File? - id: mappingstats_6 outputSource: - star_rsem_wf_pe_6/mappingstats type: File? - id: Log.progress.out_6 outputSource: - star_rsem_wf_pe_6/Log.progress.out type: File? - id: Log.out_6 outputSource: - star_rsem_wf_pe_6/Log.out type: File? - id: isoforms_result_6 outputSource: - star_rsem_wf_pe_6/isoforms_result type: File - id: genes_result_6 outputSource: - star_rsem_wf_pe_6/genes_result type: File - id: fastqFiles_6 outputSource: - star_rsem_wf_pe_6/fastqFiles type: "File[]" - id: bamRemDups_6 outputSource: - star_rsem_wf_pe_6/bamRemDups type: File? - id: aligned_6 outputSource: - star_rsem_wf_pe_6/aligned type: File - id: output outputSource: - deseq2/output type: Directory steps: - id: gunzip in: - id: file source: wget/downloaded out: - id: decompressed - id: stderr run: ../../../tool/gunzip/gunzip.cwl - id: gunzip_1 in: - id: file source: wget_1/downloaded out: - id: decompressed - id: stderr run: ../../../tool/gunzip/gunzip.cwl - id: star_index in: - id: genomeDir source: for_star_index_dir_sh/STAR_reference - id: genomeFastaFiles source: gunzip_1/decompressed - id: runThreadN source: runThreadN - id: sjdbGTFfile source: gunzip/decompressed out: - id: starIndex run: ../../../tool/star/star_index/star_index.cwl label: "STAR genomeGenerate: Generating genome indexes." - id: rsem_index in: - id: gtf source: gunzip/decompressed - id: reference_fasta source: gunzip_1/decompressed - id: num_threads source: num_threads - id: reference_dir source: for_rsem_index_dir_sh/RSEM_reference - id: reference_prefix source: reference_prefix out: - id: rsem_index run: ../../../tool/rsem/rsem_index/rsem_index.cwl label: "rsem-prepare-reference: preparing reference sequences" - id: for_star_index_dir_sh in: [] out: - id: STAR_reference run: ../../../tool/mkdir_star/mkdir_star.cwl label: mkdir_star - id: for_rsem_index_dir_sh in: [] out: - id: RSEM_reference run: ../../../tool/mkdir_rsem/mkdir_rsem.cwl label: mkdir_rsem - id: deseq2 in: - id: sample2condition.txt source: sample2condition/output1 - id: target2gene.txt source: target2gene/target2gene.txt - id: rsem_out source: - star_rsem_wf_pe/genes_result - star_rsem_wf_pe_1/genes_result - star_rsem_wf_pe_2/genes_result - star_rsem_wf_pe_3/genes_result - star_rsem_wf_pe_4/genes_result - star_rsem_wf_pe_5/genes_result - star_rsem_wf_pe_6/genes_result out: - id: output run: ../../../tool/deseq2/deseq2.cwl label: deseq2 - id: target2gene in: [] out: - id: target2gene.txt run: ../../../tool/target2gene/target2gene.cwl label: target2gene - id: sample2condition in: - id: SraRunTable source: SraRunTable out: - id: output1 run: ../../../tool/sample2condition/sample2condition.cwl label: sample2condition - id: wget in: - id: output_name source: output_name - id: url source: url out: - id: downloaded - id: stderr run: ../../../tool/wget/wget.cwl - id: wget_1 in: - id: output_name source: output_name_1 - id: url source: url_1 out: - id: downloaded - id: stderr run: ../../../tool/wget/wget.cwl - id: star_rsem_wf_pe in: - id: split_files source: split_files - id: runid source: runid - id: nthreads source: nthreads - id: genomeDir source: star_index/starIndex - id: nthreads_1 source: nthreads - id: outFileNamePrefix source: runid - id: outSAMtype source: - outSAMtype - id: quantMode source: quantMode - id: rsem_index_dir source: rsem_index/rsem_index - id: rsem_output_prefix source: runid - id: nthreads_2 source: nthreads - id: rsem_index_prefix source: rsem_index_prefix out: - id: fastqFiles - id: SJ.out.tab - id: readspergene - id: mappingstats - id: Log.progress.out - id: Log.out - id: bamRemDups - id: transcript_sorted_bam_bai - id: transcript_sorted_bam - id: transcript_bam - id: stat - id: isoforms_result - id: genes_result - id: aligned - id: transcriptomesam run: ../rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl - id: star_rsem_wf_pe_1 in: - id: split_files source: split_files - id: runid source: runid_1 - id: nthreads source: nthreads_1 - id: genomeDir source: star_index/starIndex - id: nthreads_1 source: nthreads_1 - id: outFileNamePrefix source: runid_1 - id: outSAMtype source: - outSAMtype - id: quantMode source: quantMode - id: rsem_index_dir source: rsem_index/rsem_index - id: rsem_output_prefix source: runid_1 - id: nthreads_2 source: nthreads_1 - id: rsem_index_prefix source: rsem_index_prefix out: - id: fastqFiles - id: SJ.out.tab - id: readspergene - id: mappingstats - id: Log.progress.out - id: Log.out - id: bamRemDups - id: transcript_sorted_bam_bai - id: transcript_sorted_bam - id: transcript_bam - id: stat - id: isoforms_result - id: genes_result - id: aligned - id: transcriptomesam run: ../rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl - id: star_rsem_wf_pe_2 in: - id: split_files source: split_files - id: runid source: runid_2 - id: nthreads source: nthreads_2 - id: genomeDir source: star_index/starIndex - id: nthreads_1 source: nthreads_2 - id: outFileNamePrefix source: runid_2 - id: outSAMtype source: - outSAMtype - id: quantMode source: quantMode - id: rsem_index_dir source: rsem_index/rsem_index - id: rsem_output_prefix source: runid_2 - id: nthreads_2 source: nthreads_2 - id: rsem_index_prefix source: rsem_index_prefix out: - id: fastqFiles - id: SJ.out.tab - id: readspergene - id: mappingstats - id: Log.progress.out - id: Log.out - id: bamRemDups - id: transcript_sorted_bam_bai - id: transcript_sorted_bam - id: transcript_bam - id: stat - id: isoforms_result - id: genes_result - id: aligned - id: transcriptomesam run: ../rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl - id: star_rsem_wf_pe_3 in: - id: split_files source: split_files - id: runid source: runid_3 - id: nthreads source: nthreads_3 - id: genomeDir source: star_index/starIndex - id: nthreads_1 source: nthreads_3 - id: outFileNamePrefix source: runid_3 - id: outSAMtype source: - outSAMtype - id: quantMode source: quantMode - id: rsem_index_dir source: rsem_index/rsem_index - id: rsem_output_prefix source: runid_3 - id: nthreads_2 source: nthreads_3 - id: rsem_index_prefix source: rsem_index_prefix out: - id: fastqFiles - id: SJ.out.tab - id: readspergene - id: mappingstats - id: Log.progress.out - id: Log.out - id: bamRemDups - id: transcript_sorted_bam_bai - id: transcript_sorted_bam - id: transcript_bam - id: stat - id: isoforms_result - id: genes_result - id: aligned - id: transcriptomesam run: ../rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl - id: star_rsem_wf_pe_4 in: - id: split_files source: split_files - id: runid source: runid_4 - id: nthreads source: nthreads_4 - id: genomeDir source: star_index/starIndex - id: nthreads_1 source: nthreads_4 - id: outFileNamePrefix source: runid_4 - id: outSAMtype source: - outSAMtype - id: quantMode source: quantMode - id: rsem_index_dir source: rsem_index/rsem_index - id: rsem_output_prefix source: runid_4 - id: nthreads_2 source: nthreads_4 - id: rsem_index_prefix source: rsem_index_prefix out: - id: fastqFiles - id: SJ.out.tab - id: readspergene - id: mappingstats - id: Log.progress.out - id: Log.out - id: bamRemDups - id: transcript_sorted_bam_bai - id: transcript_sorted_bam - id: transcript_bam - id: stat - id: isoforms_result - id: genes_result - id: aligned - id: transcriptomesam run: ../rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl - id: star_rsem_wf_pe_5 in: - id: split_files source: split_files - id: runid source: runid_5 - id: nthreads source: nthreads_5 - id: genomeDir source: star_index/starIndex - id: nthreads_1 source: nthreads_5 - id: outFileNamePrefix source: runid_5 - id: outSAMtype source: - outSAMtype - id: quantMode source: quantMode - id: rsem_index_dir source: rsem_index/rsem_index - id: rsem_output_prefix source: runid_5 - id: nthreads_2 source: nthreads_5 - id: rsem_index_prefix source: rsem_index_prefix out: - id: fastqFiles - id: SJ.out.tab - id: readspergene - id: mappingstats - id: Log.progress.out - id: Log.out - id: bamRemDups - id: transcript_sorted_bam_bai - id: transcript_sorted_bam - id: transcript_bam - id: stat - id: isoforms_result - id: genes_result - id: aligned - id: transcriptomesam run: ../rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl - id: star_rsem_wf_pe_6 in: - id: split_files source: split_files - id: runid source: runid_6 - id: nthreads source: nthreads_6 - id: genomeDir source: star_index/starIndex - id: nthreads_1 source: nthreads_6 - id: outFileNamePrefix source: runid_6 - id: outSAMtype source: - outSAMtype - id: quantMode source: quantMode - id: rsem_index_dir source: rsem_index/rsem_index - id: rsem_output_prefix source: runid_6 - id: nthreads_2 source: nthreads_6 - id: rsem_index_prefix source: rsem_index_prefix out: - id: fastqFiles - id: SJ.out.tab - id: readspergene - id: mappingstats - id: Log.progress.out - id: Log.out - id: bamRemDups - id: transcript_sorted_bam_bai - id: transcript_sorted_bam - id: transcript_bam - id: stat - id: isoforms_result - id: genes_result - id: aligned - id: transcriptomesam run: ../rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl requirements: - class: SubworkflowFeatureRequirement - class: MultipleInputFeatureRequirement $schemas: - "https://schema.org/version/latest/schemaorg-current-http.rdf" - "http://edamontology.org/EDAM_1.18.owl" "s:author": - class: "s:Person" "s:email": "mailto:inutano@gmail.com" "s:identifier": "https://orcid.org/0000-0003-3777-5945" "s:name": Tazro Ohta "s:codeRepository": "https://github.com/pitagora-network/pitagora-cwl" "s:license": "https://spdx.org/licenses/Apache-2.0"