pipeline-se-revstranded-with-sjdb.cwl

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
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
   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
     run: 03-map-se-with-sjdb.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_star2
     - pcr_bottleneck_coef_file
   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