CWL Workflow: pipeline-pe-umis.cwl

Workflow: pipeline-pe-umis.cwl

Fetched 2024-11-25 23:53:55 GMT

Verified with cwltool version 3.1.20221201130942

STARR-seq pipeline - reads: PE

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This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Doc
nthreads_qc	Integer	Number of threads - qc.
nthreads_map	Integer	Number of threads - map.
fgbio_jar_path	String	fgbio Java jar file
nthreads_quant	Integer	Number of threads - quantification.
nthreads_trimm	Integer	Number of threads - trim.
picard_jar_path	String	Picard Java jar file
picard_java_opts	String (Optional)	JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")
regions_bed_file	File	Regions bed file used to filter-in reads (used in samtools, for example chromosomes of interest)
genome_sizes_file	File	Genome sizes tab-delimited file (used in samtools)
trimmomatic_jar_path	String	Trimmomatic Java jar file
default_adapters_file	File	Adapters file
input_fastq_umi_files	File[]	Input fastq with UMIs files
trimmomatic_java_opts	String (Optional)	JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")
input_fastq_read1_files	File[]	Input read1 fastq files
input_fastq_read2_files	File[]	Input read2 fastq files
ENCODE_blacklist_bedfile	File	Bedfile containing ENCODE consensus blacklist regions to be excluded.
genome_ref_first_index_file	File	\"First index file of Bowtie2 reference genome with extension 1.bt2. \ (Note: the rest of the index files MUST be in the same folder)\"

Steps

ID	Runs	Doc
qc	01-qc-pe.cwl (Workflow)	STARR-seq 01 QC - reads: PE
map	03-map-pe-umis.cwl (Workflow)	STARR-seq 03 mapping - reads: PE
trim	02-trim-pe.cwl (Workflow)	STARR-seq 02 trimming - reads: PE
quant	04-quantification.cwl (Workflow)	STARR-seq 04 quantification

Outputs

ID	Type	Doc
map_bowtie_log_files	File[]	Bowtie log file with mapping stats
map_preseq_c_curve_files	File[]	Preseq c_curve output files
map_unmapped_fastq_files	File[]	Gzip compressed FASTQ ummaped and unpaired sequences
output_diff_counts_read1	File[]
output_diff_counts_read2	File[]
quant_bw_dedup_raw_files	File[]	Signal files with 1bp raw read pileup ignoring duplicates.
map_dups_marked_bam_files	File[]	Filtered BAM files with duplicates marked (post-processing end point)
map_mark_duplicates_files	File[]	Summary of duplicates removed with Picard tool MarkDuplicates (for multiple reads aligned to the same positions)
quant_bw_dedup_norm_files	File[]	Signal files with RPKM normalization ignoring duplicates.
map_genomic_template_files	File[]	BEDPE files with fragment/template coordinates
output_count_raw_reads_read1	File[]
output_count_raw_reads_read2	File[]
output_custom_adapters_read1	File[]
output_custom_adapters_read2	File[]
quant_bw_with_dups_norm_files	File[]	Signal files with RPKM normalization including duplicates.
output_fastqc_data_files_read1	File[]	FastQC data files for paired read 1
output_fastqc_data_files_read2	File[]	FastQC data files for paired read 2
output_fastqc_report_files_read1	File[]	FastQC reports in zip format for paired read 1
output_fastqc_report_files_read2	File[]	FastQC reports in zip format for paired read 2
output_data_fastq_read1_trimmed_files	File[]	Trimmed fastq files for paired read 1
output_data_fastq_read2_trimmed_files	File[]	Trimmed fastq files for paired read 2
output_trimmed_read1_fastq_read_count	File[]	Trimmed read counts of paired read 1 fastq files
output_trimmed_read2_fastq_read_count	File[]	Trimmed read counts of paired read 2 fastq files

Permalink: https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/STARR-seq_pipeline/pipeline-pe-umis.cwl