Workflow: epigenome-chip-seq.packed.cwl#macs2.cwl
Fetched 2023-01-09 14:00:16 GMT
Verified with cwltool version 3.1.20221201130942
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This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq | File | ||
| nthreads | Integer | ||
| macs2_p_value | Float | ||
| macs2_organism | String | mouse: mm, human: hs | |
| macs2_control_bam | File | ||
| bowtie2_genome_index | File | ||
| samtools_skip_alignments | Integer | ||
| samtools_filter_alignments | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastp |
epigenome-chip-seq.packed.cwl#fastp-se-html.cwl
(CommandLineTool)
|
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...) |
|
| macs2 |
epigenome-chip-seq.packed.cwl#MACS2-callpeak.cwl
(CommandLineTool)
|
||
| fastqc |
epigenome-chip-seq.packed.cwl#fastqc.cwl
(CommandLineTool)
|
FastQC: A quality control tool for high throughput sequence data |
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| bowtie2 |
epigenome-chip-seq.packed.cwl#bowtie2-se.cwl
(CommandLineTool)
|
A fast and sensitive gapped read aligner |
|
| samtools-view |
epigenome-chip-seq.packed.cwl#samtools-view.cwl
(CommandLineTool)
|
samtools view to convert sam format to bam format |
|
| samtools-index |
epigenome-chip-seq.packed.cwl#samtools-index.cwl
(CommandLineTool)
|
samtools index to create index for given bam file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastp-html | File | ||
| bowtie2-sam | File | ||
| fastqc-result | File[] | ||
| macs2-model-r | File | ||
| macs2-peaks-xls | File | ||
| macs2-summits-bed | File | ||
| samtools-view-bam | File | ||
| fastp-trimmed-fastq | File | ||
| macs2-treat-pileup-bdg | File | ||
| macs2-peaks-narrow-peak | File | ||
| macs2-control-lambda-bdg | File | ||
| samtools-index-bam-index | File |
Permalink:
https://w3id.org/cwl/view/git/dad35f6d3743aa92b751333bd2e15cda259d4d43/workflow/epigenome-chip-seq/epigenome-chip-seq.packed.cwl?part=macs2.cwl
