Workflow: wf_clipseqcore_se_1barcode.cwl

Fetched 2022-01-20 13:34:52 GMT
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ID Type Title Doc
chrom_sizes File
speciesGenomeDir Directory
repeatElementGenomeDir Directory
species String
dataset String


ID Runs Label Doc
makebigwigfiles.cwl (CommandLineTool)

Creates strand-specific bigwig files from a BAM file. See original script here: Usage: makebigwigfiles --bam BAM --genome GENOME --dont_flip --bw_pos --bw_neg


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)


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


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