class: Workflow cwlVersion: v1.0 doc: 'STARR-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[] input_fastq_umi_files: doc: Input fastq with UMIs files type: File[] fgbio_jar_path: default: /opt/fgbio.jar doc: fgbio Java jar file type: string genome_sizes_file: doc: Genome sizes tab-delimited file (used in samtools) type: File ENCODE_blacklist_bedfile: doc: Bedfile containing ENCODE consensus blacklist regions to be excluded. type: File regions_bed_file: doc: Regions bed file used to filter-in reads (used in samtools, for example chromosomes of interest) type: File genome_ref_first_index_file: doc: '"First index file of Bowtie2 reference genome with extension 1.bt2. \ (Note: the rest of the index files MUST be in the same folder)" ' type: File secondaryFiles: - ^^.2.bt2 - ^^.3.bt2 - ^^.4.bt2 - ^^.rev.1.bt2 - ^^.rev.2.bt2 nthreads_qc: doc: Number of threads - qc. type: int nthreads_trimm: doc: Number of threads - trim. type: int nthreads_map: doc: Number of threads - map. type: int nthreads_quant: doc: Number of threads - quantification. type: int default_adapters_file: doc: Adapters file type: File trimmomatic_jar_path: doc: Trimmomatic Java jar file type: string trimmomatic_java_opts: doc: JVM arguments should be a quoted, space separated list (e.g. "-Xms128m -Xmx512m") type: string? picard_java_opts: doc: JVM arguments should be a quoted, space separated list (e.g. "-Xms128m -Xmx512m") type: string? picard_jar_path: doc: Picard Java jar file 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 map_mark_duplicates_files: doc: Summary of duplicates removed with Picard tool MarkDuplicates (for multiple reads aligned to the same positions) type: File[] outputSource: map/output_picard_mark_duplicates_files map_dups_marked_bam_files: doc: Filtered BAM files with duplicates marked (post-processing end point) type: File[] outputSource: map/output_data_bam_files map_unmapped_fastq_files: doc: Gzip compressed FASTQ ummaped and unpaired sequences type: File[] outputSource: map/output_data_unmapped_fastq_files map_bowtie_log_files: doc: Bowtie log file with mapping stats type: File[] outputSource: map/output_bowtie_log map_genomic_template_files: doc: BEDPE files with fragment/template coordinates type: File[] outputSource: map/output_templates_files map_preseq_c_curve_files: doc: Preseq c_curve output files type: File[] outputSource: map/output_preseq_c_curve_files quant_bw_dedup_norm_files: doc: Signal files with RPKM normalization ignoring duplicates. type: File[] outputSource: quant/bw_dedup_norm_files quant_bw_dedup_raw_files: doc: Signal files with 1bp raw read pileup ignoring duplicates. type: File[] outputSource: quant/bw_dedup_raw_files quant_bw_with_dups_norm_files: doc: Signal files with RPKM normalization including duplicates. type: File[] outputSource: quant/bw_with_dups_norm_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 input_fastq_umi_files: input_fastq_umi_files genome_sizes_file: genome_sizes_file ENCODE_blacklist_bedfile: ENCODE_blacklist_bedfile regions_bed_file: regions_bed_file genome_ref_first_index_file: genome_ref_first_index_file picard_jar_path: picard_jar_path picard_java_opts: picard_java_opts nthreads: nthreads_map fgbio_jar_path: fgbio_jar_path run: 03-map-pe-umis.cwl out: - output_data_bam_files - output_data_dedup_bam_files - output_picard_mark_duplicates_files - output_data_unmapped_fastq_files - output_bowtie_log - output_preseq_c_curve_files - output_templates_files quant: in: input_bam_files: map/output_data_bam_files input_dedup_bam_files: map/output_data_dedup_bam_files ENCODE_blacklist_bedfile: ENCODE_blacklist_bedfile nthreads: nthreads_quant run: 04-quantification.cwl out: - bw_dedup_norm_files - bw_with_dups_norm_files - bw_dedup_raw_files