- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 3-clause "New" or "Revised" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
read | |||
dataset | String | ||
species | String | ||
chrom_sizes | File | ||
speciesGenomeDir | Directory | ||
repeatElementGenomeDir | Directory |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
demultiplex |
wf_demultiplex_se.cwl
(Workflow)
|
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) |
|
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 |
|
b1_trim_and_map |
wf_trim_and_map_se.cwl
(Workflow)
|
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 |
---|---|---|---|
output_neg_bw | File | ||
output_pos_bw | File | ||
b1_trimx1_fastq | File[] | ||
b1_trimx2_fastq | File[] | ||
b1_trimx1_metrics | File | ||
b1_trimx2_metrics | File | ||
b1_mapgenome_stats | File | ||
b1_demuxed_fastq_r1 | File | ||
b1_maprepeats_stats | File | ||
b1_trimx1_fastqc_stats | File | ||
b1_trimx2_fastqc_stats | File | ||
b1_trimx1_fastqc_report | File | ||
b1_trimx2_fastqc_report | File | ||
b1_sorted_unmapped_fastq | File | ||
b1_mapgenome_star_settings | File | ||
b1_output_rmdup_sorted_bam | File | ||
b1_maprepeats_star_settings | File | ||
b1_mapgenome_mapped_to_genome | File | ||
b1_maprepeats_mapped_to_genome | File | ||
b1_output_pre_rmdup_sorted_bam | File | ||
b1_output_barcodecollapsese_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/49a9bcda10de8f55fab2481f424eb9cdf2e5b256/cwl/wf_clipseqcore_se_1barcode.cwl