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| #!/usr/bin/env cwl-runner | |
| class: Workflow | |
| cwlVersion: v1.0 | |
| doc: RNA-seq 04 quantification | |
| requirements: | |
| - class: ScatterFeatureRequirement | |
| - class: StepInputExpressionRequirement | |
| - class: InlineJavascriptRequirement | |
| - class: SubworkflowFeatureRequirement | |
| inputs: | |
| input_bam_files: | |
| type: File[] | |
| nthreads: | |
| default: 1 | |
| type: int | |
| rsem_reference_files: | |
| doc: RSEM genome reference files - generated with the rsem-prepare-reference command | |
| type: Directory | |
| annotation_file: | |
| doc: GTF annotation file | |
| type: File | |
| input_transcripts_bam_files: | |
| type: File[] | |
| input_genome_sizes: | |
| type: File | |
| bamtools_forward_filter_file: | |
| doc: JSON filter file for forward strand used in bamtools (see bamtools-filter command) | |
| type: File | |
| bamtools_reverse_filter_file: | |
| doc: JSON filter file for reverse strand used in bamtools (see bamtools-filter command) | |
| type: File | |
| outputs: | |
| featurecounts_counts: | |
| doc: Normalized fragment extended reads bigWig (signal) files | |
| type: File[] | |
| outputSource: featurecounts/output_files | |
| rsem_isoforms_files: | |
| doc: RSEM isoforms files | |
| type: File[] | |
| outputSource: rsem-calc-expr/isoforms | |
| rsem_genes_files: | |
| doc: RSEM genes files | |
| type: File[] | |
| outputSource: rsem-calc-expr/genes | |
| bam_plus_files: | |
| doc: BAM files containing only reads in the forward (plus) strand. | |
| type: File[] | |
| outputSource: split_bams/bam_plus_files | |
| bw_raw_plus_files: | |
| doc: Raw bigWig files from BAM files containing only reads in the forward (plus) strand. | |
| type: File[] | |
| outputSource: bdg2bw-raw-plus/output_bigwig | |
| bw_norm_plus_files: | |
| doc: Normalized by RPKM bigWig files from BAM files containing only reads in the forward (plus) strand. | |
| type: File[] | |
| outputSource: bamcoverage-plus/output_bam_coverage | |
| bam_minus_files: | |
| doc: BAM files containing only reads in the reverse (minus) strand. | |
| type: File[] | |
| outputSource: split_bams/bam_minus_files | |
| bw_raw_minus_files: | |
| doc: Raw bigWig files from BAM files containing only reads in the reverse (minus) strand. | |
| type: File[] | |
| outputSource: bdg2bw-raw-minus/output_bigwig | |
| bw_norm_minus_files: | |
| doc: Normalized by RPKM bigWig files from BAM files containing only reads in the forward (plus) strand. | |
| type: File[] | |
| outputSource: bdg2bw-norm-minus/output_bigwig | |
| steps: | |
| basename: | |
| run: ../utils/basename.cwl | |
| in: | |
| file_path: | |
| source: input_bam_files | |
| valueFrom: $(self.basename) | |
| sep: | |
| valueFrom: \.Aligned\.out\.sorted | |
| scatter: file_path | |
| out: | |
| - basename | |
| featurecounts: | |
| run: ../quant/subread-featurecounts.cwl | |
| in: | |
| B: | |
| valueFrom: ${return true} | |
| g: | |
| valueFrom: gene_id | |
| output_filename: | |
| source: basename/basename | |
| valueFrom: $(self + ".featurecounts.counts.txt") | |
| p: | |
| valueFrom: ${return true} | |
| s: | |
| valueFrom: ${return 1} | |
| t: | |
| valueFrom: exon | |
| annotation_file: annotation_file | |
| T: nthreads | |
| input_files: | |
| source: input_bam_files | |
| valueFrom: ${if (Array.isArray(self)) return self; return [self]; } | |
| scatterMethod: dotproduct | |
| scatter: | |
| - input_files | |
| - output_filename | |
| out: | |
| - output_files | |
| rsem-calc-expr: | |
| run: ../quant/rsem-calculate-expression.cwl | |
| in: | |
| reference_name: | |
| source: rsem_reference_files | |
| valueFrom: | | |
| ${ | |
| var trans_file_str = self.listing.map(function(e){return e.location}).filter(function(e){return e.match(/\.transcripts\.fa$/)})[0]; | |
| return trans_file_str.match(/.*[\\\\\\/](.*)\.transcripts\.fa$/)[1]; | |
| } | |
| reference_files: rsem_reference_files | |
| no-bam-output: | |
| valueFrom: ${return true} | |
| quiet: | |
| valueFrom: ${return true} | |
| seed: | |
| valueFrom: ${return 1234} | |
| sample_name: | |
| source: basename/basename | |
| valueFrom: $(self + ".rsem") | |
| bam: input_transcripts_bam_files | |
| num-threads: nthreads | |
| paired-end: | |
| valueFrom: ${return true} | |
| strand-specific: | |
| valueFrom: ${return true} | |
| scatterMethod: dotproduct | |
| scatter: | |
| - bam | |
| - sample_name | |
| out: | |
| - isoforms | |
| - genes | |
| - rsem_stat | |
| split_bams: | |
| in: | |
| bamtools_reverse_filter_file: bamtools_reverse_filter_file | |
| bamtools_forward_filter_file: bamtools_forward_filter_file | |
| input_bam_files: input_bam_files | |
| input_basenames: basename/basename | |
| run: ../quant/split-bams-by-strand-and-index.cwl | |
| out: | |
| - bam_plus_files | |
| - bam_minus_files | |
| bamcoverage-minus: | |
| run: ../quant/deeptools-bamcoverage.cwl | |
| scatter: bam | |
| in: | |
| binSize: | |
| valueFrom: ${return 1} | |
| numberOfProcessors: nthreads | |
| bam: split_bams/bam_minus_files | |
| output_suffix: | |
| valueFrom: .norm-minus-pre-negated-bw | |
| normalizeUsing: | |
| valueFrom: RPKM | |
| out: | |
| - output_bam_coverage | |
| bw2bdg-minus: | |
| run: ../quant/bigWigToBedGraph.cwl | |
| scatter: bigwig_file | |
| in: | |
| bigwig_file: bamcoverage-minus/output_bam_coverage | |
| out: | |
| - output_bedgraph | |
| negate_minus_bdg_norm: | |
| run: ../quant/negate-minus-strand-bedgraph.cwl | |
| scatter: | |
| - bedgraph_file | |
| - output_filename | |
| scatterMethod: dotproduct | |
| in: | |
| bedgraph_file: bw2bdg-minus/output_bedgraph | |
| output_filename: | |
| source: basename/basename | |
| valueFrom: $(self + ".norm-minus-bdg") | |
| out: | |
| - negated_minus_bdg | |
| bdg2bw-raw-minus: | |
| run: ../quant/bedGraphToBigWig.cwl | |
| scatter: bed_graph | |
| in: | |
| output_suffix: | |
| valueFrom: .bw | |
| genome_sizes: input_genome_sizes | |
| bed_graph: negate_minus_bdg/negated_minus_bdg | |
| out: | |
| - output_bigwig | |
| bdg2bw-norm-minus: | |
| run: ../quant/bedGraphToBigWig.cwl | |
| scatter: bed_graph | |
| in: | |
| output_suffix: | |
| valueFrom: .Aligned.minus.norm.bw | |
| genome_sizes: input_genome_sizes | |
| bed_graph: negate_minus_bdg_norm/negated_minus_bdg | |
| out: | |
| - output_bigwig | |
| bedtools_genomecov_minus: | |
| run: ../map/bedtools-genomecov.cwl | |
| scatter: ibam | |
| in: | |
| bg: | |
| valueFrom: ${return true} | |
| g: input_genome_sizes | |
| ibam: split_bams/bam_minus_files | |
| out: | |
| - output_bedfile | |
| bedsort_genomecov_minus: | |
| run: ../quant/bedSort.cwl | |
| scatter: bed_file | |
| in: | |
| bed_file: bedtools_genomecov_minus/output_bedfile | |
| out: | |
| - bed_file_sorted | |
| negate_minus_bdg: | |
| run: ../quant/negate-minus-strand-bedgraph.cwl | |
| scatterMethod: dotproduct | |
| scatter: | |
| - bedgraph_file | |
| - output_filename | |
| in: | |
| bedgraph_file: bedsort_genomecov_minus/bed_file_sorted | |
| output_filename: | |
| source: basename/basename | |
| valueFrom: $(self + ".Aligned.minus.raw.bdg") | |
| out: | |
| - negated_minus_bdg | |
| bamcoverage-plus: | |
| run: ../quant/deeptools-bamcoverage.cwl | |
| scatter: bam | |
| in: | |
| binSize: | |
| valueFrom: ${return 1} | |
| numberOfProcessors: nthreads | |
| bam: split_bams/bam_plus_files | |
| output_suffix: | |
| valueFrom: .norm.bw | |
| normalizeUsing: | |
| valueFrom: RPKM | |
| out: | |
| - output_bam_coverage | |
| bedtools_genomecov_plus: | |
| run: ../map/bedtools-genomecov.cwl | |
| scatter: ibam | |
| in: | |
| bg: | |
| valueFrom: ${return true} | |
| g: input_genome_sizes | |
| ibam: split_bams/bam_plus_files | |
| out: | |
| - output_bedfile | |
| bdg2bw-raw-plus: | |
| run: ../quant/bedGraphToBigWig.cwl | |
| scatter: bed_graph | |
| in: | |
| output_suffix: | |
| valueFrom: .raw.bw | |
| genome_sizes: input_genome_sizes | |
| bed_graph: bedsort_genomecov_plus/bed_file_sorted | |
| out: | |
| - output_bigwig | |
| bedsort_genomecov_plus: | |
| run: ../quant/bedSort.cwl | |
| scatter: bed_file | |
| in: | |
| bed_file: bedtools_genomecov_plus/output_bedfile | |
| out: | |
| - bed_file_sorted |