class: Workflow cwlVersion: v1.0 doc: 'RNA-seq pipeline - reads: PE' requirements: - class: ScatterFeatureRequirement - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: input_fastq_read1_files: doc: Input read1 fastq files type: File[] genome_sizes_file: doc: Genome sizes tab-delimited file (used in samtools) type: File nthreads_qc: doc: Number of threads - qc. type: int nthreads_quant: doc: Number of threads - quantification. type: int default_adapters_file: doc: Adapters file type: File trimmomatic_java_opts: doc: JVM arguments should be a quoted, space separated list (e.g. "-Xms128m -Xmx512m") type: string? rsem_reference_files: doc: RSEM genome reference files - generated with the rsem-prepare-reference command type: Directory nthreads_trimm: doc: Number of threads - trim. type: int STARgenomeDir: doc: STAR genome reference/indices directory. type: Directory nthreads_map: doc: Number of threads - map. type: int annotation_file: doc: GTF annotation file type: File genome_fasta_files: doc: STAR genome generate - Genome FASTA file with all the genome sequences in FASTA format type: File[] trimmomatic_jar_path: doc: Trimmomatic Java jar file type: string sjdbOverhang: doc: Length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. type: string sjdb_name: default: ggr.SJ.out.all.tab type: string outputs: output_fastqc_report_files_read1: doc: FastQC reports in zip format for paired read 1 type: File[] outputSource: qc/output_fastqc_report_files_read1 output_fastqc_data_files_read1: doc: FastQC data files for paired read 1 type: File[] outputSource: qc/output_fastqc_data_files_read1 output_count_raw_reads_read1: outputSource: qc/output_count_raw_reads_read1 type: File[] output_custom_adapters_read1: outputSource: qc/output_custom_adapters_read1 type: File[] output_diff_counts_read1: outputSource: qc/output_diff_counts_read1 type: File[] output_trimmed_read1_fastq_read_count: doc: Trimmed read counts of paired read 1 fastq files type: File[] outputSource: trim/output_trimmed_read1_fastq_read_count output_data_fastq_read1_trimmed_files: doc: Trimmed fastq files for paired read 1 type: File[] outputSource: trim/output_data_fastq_read1_trimmed_files star_aligned_sorted_file: doc: STAR mapped sorted file. type: File[] outputSource: map/star_aligned_sorted_file star1_stat_files: doc: STAR pass-1 stat files. type: items: - 'null' - items: File type: array type: array outputSource: map/star1_stat_files read_count_mapped_star1: doc: Read counts of the mapped BAM files after STAR pass1 type: File[] outputSource: map/read_count_mapped_star1 star_1pass_sjdb: doc: SJDB from union of STAR 1st pass type: File outputSource: map/star_1pass_sjdb generated_genome_files: doc: STAR generated genome files type: File? outputSource: map/generated_genome_files percentage_uniq_reads_star1: doc: Percentage of uniq reads from preseq c_curve output type: File[] outputSource: map/percentage_uniq_reads_star1 pcr_bottleneck_coef_file: doc: PCR Bottleneck Coefficient type: File[] outputSource: map/pcr_bottleneck_coef_file read_count_mapped_star2: doc: Read counts of the mapped BAM files after STAR pass2 type: File[] outputSource: map/read_count_mapped_star2 read_count_transcriptome_mapped_star2: doc: Read counts of the mapped to transcriptome BAM files after STAR pass1 type: File[] outputSource: map/read_count_transcriptome_mapped_star2 star2_readspergene_file: doc: STAR pass-2 reads per gene counts file. type: File[]? outputSource: map/star2_readspergene_file star2_stat_files: doc: STAR pass-2 stat files. type: items: - 'null' - items: File type: array type: array outputSource: map/star2_stat_files transcriptome_star_aligned_file: doc: STAR mapped to transcriptome sorted file. type: File[] outputSource: map/transcriptome_star_aligned_file transcriptome_star_stat_files: doc: STAR pass-2 aligned to transcriptome stat files. type: items: - 'null' - items: File type: array type: array outputSource: map/transcriptome_star_stat_files featurecounts_counts: doc: Normalized fragment extended reads bigWig (signal) files type: File[] outputSource: quant/featurecounts_counts rsem_isoforms_files: doc: RSEM isoforms files type: File[] outputSource: quant/rsem_isoforms_files rsem_genes_files: doc: RSEM genes files type: File[] outputSource: quant/rsem_genes_files bw_raw_files: doc: Raw bigWig files. type: File[] outputSource: quant/bw_raw_files bw_norm_files: doc: Normalized by RPKM bigWig files. type: File[] outputSource: quant/bw_norm_files steps: qc: in: input_fastq_read1_files: input_fastq_read1_files default_adapters_file: default_adapters_file nthreads: nthreads_qc run: 01-qc-se.cwl out: - output_fastqc_report_files_read1 - output_fastqc_data_files_read1 - output_custom_adapters_read1 - output_count_raw_reads_read1 - output_diff_counts_read1 trim: in: input_read1_adapters_files: qc/output_custom_adapters_read1 input_fastq_read1_files: input_fastq_read1_files nthreads: nthreads_trimm trimmomatic_java_opts: trimmomatic_java_opts trimmomatic_jar_path: trimmomatic_jar_path run: 02-trim-se.cwl out: - output_data_fastq_read1_trimmed_files - output_trimmed_read1_fastq_read_count map: in: input_fastq_read1_files: trim/output_data_fastq_read1_trimmed_files genome_sizes_file: genome_sizes_file genome_fasta_files: genome_fasta_files STARgenomeDir: STARgenomeDir annotation_file: annotation_file sjdbOverhang: sjdbOverhang nthreads: nthreads_map sjdb_name: sjdb_name run: 03-map-se.cwl out: - star_aligned_sorted_file - star2_stat_files - star2_readspergene_file - read_count_mapped_star2 - transcriptome_star_aligned_file - transcriptome_star_stat_files - read_count_transcriptome_mapped_star2 - percentage_uniq_reads_star1 - pcr_bottleneck_coef_file - generated_genome_files - star1_stat_files - read_count_mapped_star1 - star_1pass_sjdb quant: in: input_bam_files: map/star_aligned_sorted_file input_transcripts_bam_files: map/transcriptome_star_aligned_file annotation_file: annotation_file input_genome_sizes: genome_sizes_file rsem_reference_files: rsem_reference_files nthreads: nthreads_quant run: 04-quantification-se-revstranded.cwl out: - featurecounts_counts - rsem_isoforms_files - rsem_genes_files - bw_raw_files - bw_norm_files