CWL Workflow: pipeline-se.cwl

Workflow: pipeline-se.cwl

Fetched 2023-01-04 17:55:04 GMT

Verified with cwltool version 3.1.20221201130942

DNase-seq pipeline - reads: SE

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.

ID	Type	Doc
nthreads_map	Integer	Number of threads required for the 03-map step
nthreads_quant	Integer	Number of threads required for the 05-quantification step
genome_sizes_file	File	Genome sizes tab-delimited file (used in samtools)
input_fastq_files	File[]
nthreads_peakcall	Integer	Number of threads required for the 04-peakcall step
default_adapters_file	File	Adapters file
ENCODE_blacklist_bedfile	File	Bedfile containing ENCODE consensus blacklist regions to be excluded.
genome_ref_first_index_file	File	\"First index file of Bowtie reference genome with extension 1.ebwt. \ (Note: the rest of the index files MUST be in the same folder)\"

ID	Runs	Doc
map	01-map-se.cwl (Workflow)	DNase-seq 01 mapping - reads: SE
quant	03-quantification.cwl (Workflow)	DNase-seq 03 quantification
peak_call	02-peakcall.cwl (Workflow)	DNase-seq 02 quantification

ID	Type	Doc
map_pbc_files	File[]	PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5)
map_read_count	File[]	Read counts of the mapped BAM files
fastq_read_count	File[]	Read counts of the (unprocessed) input fastq files
map_bowtie_log_files	File[]	Bowtie log file with mapping stats
map_filtered_bam_files	File[]	Filtered BAM files (post-processing end point)
quant_bigwig_raw_files	File[]	Raw reads bigWig (signal) files
map_filtered_read_count	File[]	Read counts of the mapped and filtered BAM files
peak_call_peak_xls_file	File[]	Peak calling report file
quant_bigwig_norm_files	File[]	Normalized reads bigWig (signal) files
map_preseq_c_curve_files	File[]	Preseq c_curve output files
map_percentage_uniq_reads	File[]	Percentage of uniq reads from preseq c_curve output
peak_call_narrowpeak_file	File[]	Peaks in narrowPeak file format
peak_call_spp_x_cross_corr	File[]	SPP strand cross correlation summary
quant_bigwig_extended_files	File[]	Fragment extended reads bigWig (signal) files
peak_call_spp_x_cross_corr_plot	File[]	SPP strand cross correlation plot
quant_bigwig_extended_norm_files	File[]	Normalized fragment extended reads bigWig (signal) files
peak_call_extended_narrowpeak_file	File[]	Extended fragment peaks in narrowPeak file format
peak_call_filtered_read_count_file	File[]	Filtered read count after peak calling
peak_call_peak_count_within_replicate	File[]	Peak counts within replicate
peak_call_read_in_peak_count_within_replicate	File[]	Peak counts within replicate

Permalink: https://w3id.org/cwl/view/git/517487e59d240c197fc91f08d20dadca97a9e121/v1.0/DNase-seq_pipeline/pipeline-se.cwl