/
pipeline-pe-unstranded-with-sjdb.cwl
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pipeline-pe-unstranded-with-sjdb.cwl
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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[]
input_fastq_read2_files:
doc: Input read2 fastq files
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
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
output_fastqc_report_files_read2:
doc: FastQC reports in zip format for paired read 2
type: File[]
outputSource: qc/output_fastqc_report_files_read2
output_fastqc_data_files_read2:
doc: FastQC data files for paired read 2
type: File[]
outputSource: qc/output_fastqc_data_files_read2
output_count_raw_reads_read2:
outputSource: qc/output_count_raw_reads_read2
type: File[]
output_custom_adapters_read2:
outputSource: qc/output_custom_adapters_read2
type: File[]
output_diff_counts_read2:
outputSource: qc/output_diff_counts_read2
type: File[]
output_trimmed_read2_fastq_read_count:
doc: Trimmed read counts of paired read 2 fastq files
type: File[]
outputSource: trim/output_trimmed_read2_fastq_read_count
output_data_fastq_read2_trimmed_files:
doc: Trimmed fastq files for paired read 2
type: File[]
outputSource: trim/output_data_fastq_read2_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
bam_plus_files:
doc: BAM files containing only reads in the forward (plus) strand.
type: File[]
outputSource: quant/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: quant/bw_raw_plus_files
bw_norm_plus_files:
doc: Normalized by RPKM bigWig files from BAM files containing only reads in the forward (plus) strand.
type: File[]
outputSource: quant/bw_norm_plus_files
bam_minus_files:
doc: BAM files containing only reads in the reverse (minus) strand.
type: File[]
outputSource: quant/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: quant/bw_raw_minus_files
bw_norm_minus_files:
doc: Normalized by RPKM bigWig files from BAM files containing only reads in the forward (plus) strand.
type: File[]
outputSource: quant/bw_norm_minus_files
steps:
qc:
in:
input_fastq_read1_files: input_fastq_read1_files
input_fastq_read2_files: input_fastq_read2_files
default_adapters_file: default_adapters_file
nthreads: nthreads_qc
run: 01-qc-pe.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
- output_fastqc_report_files_read2
- output_fastqc_data_files_read2
- output_custom_adapters_read2
- output_count_raw_reads_read2
- output_diff_counts_read2
trim:
in:
input_read1_adapters_files: qc/output_custom_adapters_read1
input_fastq_read1_files: input_fastq_read1_files
input_read2_adapters_files: qc/output_custom_adapters_read2
input_fastq_read2_files: input_fastq_read2_files
nthreads: nthreads_trimm
trimmomatic_java_opts: trimmomatic_java_opts
trimmomatic_jar_path: trimmomatic_jar_path
run: 02-trim-pe.cwl
out:
- output_data_fastq_read1_trimmed_files
- output_trimmed_read1_fastq_read_count
- output_data_fastq_read2_trimmed_files
- output_trimmed_read2_fastq_read_count
map:
in:
input_fastq_read1_files: trim/output_data_fastq_read1_trimmed_files
input_fastq_read2_files: trim/output_data_fastq_read2_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-pe-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
bamtools_forward_filter_file: bamtools_forward_filter_file
bamtools_reverse_filter_file: bamtools_reverse_filter_file
run: 04-quantification-pe-unstranded.cwl
out:
- featurecounts_counts
- rsem_isoforms_files
- rsem_genes_files
- bam_plus_files
- bam_minus_files
- bw_raw_plus_files
- bw_raw_minus_files
- bw_norm_plus_files
- bw_norm_minus_files