Workflow: wf_clipseqcore_se_1barcode.cwl

Fetched 2022-01-20 13:34:52 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
chrom_sizes File
read
speciesGenomeDir Directory
repeatElementGenomeDir Directory
species String
dataset String

Steps

ID Runs Label Doc
make_bigwigs
makebigwigfiles.cwl (CommandLineTool)

Creates strand-specific bigwig files from a BAM file. See original script here: https://github.com/YeoLab/gscripts/blob/master/gscripts/general/make_bigwig_files_pe.py Usage: makebigwigfiles --bam BAM --genome GENOME --dont_flip --bw_pos --bw_neg

demultiplex

This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)

b1_trim_and_map

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

Outputs

ID Type Label Doc
b1_demuxed_fastq_r1 File
b1_trimx1_fastqc_report File
b1_output_pre_rmdup_sorted_bam File
b1_sorted_unmapped_fastq File
b1_trimx1_fastqc_stats File
b1_trimx2_fastqc_stats File
b1_mapgenome_star_settings File
output_pos_bw File
b1_trimx1_metrics File
b1_maprepeats_mapped_to_genome File
b1_trimx1_fastq File[]
b1_mapgenome_stats File
output_neg_bw File
b1_trimx2_fastq File[]
b1_output_barcodecollapsese_metrics File
b1_trimx2_metrics File
b1_mapgenome_mapped_to_genome File
b1_maprepeats_star_settings File
b1_maprepeats_stats File
b1_trimx2_fastqc_report File
b1_output_rmdup_sorted_bam File
Permalink: https://w3id.org/cwl/view/git/b389f7fe3e76cb6e3f31c3a8e2e3b59bb400e74c/cwl/wf_clipseqcore_se_1barcode.cwl