Workflow: epigenome-chip-seq.cwl
Fetched 2024-05-14 01:17:12 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
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 |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | 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 |
|---|---|---|---|
| macs2-fastq1 |
macs2/macs2.cwl
(Workflow)
|
string |
|
| macs2-fastq2 |
macs2/macs2.cwl
(Workflow)
|
string |
|
| bedtools-intersect-overlap |
../../tool/bedtools/bedtools_intersect_overlap/bedtools_intersect_overlap.cwl
(CommandLineTool)
|
bedtools intersect allows one to screen for overlaps between two sets of genomic features. |
|
| bedtools-intersect-no-overlap |
../../tool/bedtools/bedtools_intersect_no_overlap/bedtools_intersect_no_overlap.cwl
(CommandLineTool)
|
bedtools intersect allows one to screen for overlaps between two sets of genomic features. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastp-html-fastq1 | File | ||
| fastp-html-fastq2 | File | ||
| bowtie2-sam-fastq1 | File | ||
| bowtie2-sam-fastq2 | File | ||
| narrow-peak-overlap | File | ||
| fastqc-result-fastq1 | File[] | ||
| fastqc-result-fastq2 | File[] | ||
| macs2-model-r-fastq1 | File | ||
| macs2-model-r-fastq2 | File | ||
| macs2-peaks-xls-fastq1 | File | ||
| macs2-peaks-xls-fastq2 | File | ||
| narrow-peak-no-overlap | File | ||
| macs2-summits-bed-fastq1 | File | ||
| macs2-summits-bed-fastq2 | File | ||
| samtools-view-bam-fastq1 | File | ||
| samtools-view-bam-fastq2 | File | ||
| fastp-trimmed-fastq-fastq1 | File | ||
| fastp-trimmed-fastq-fastq2 | File | ||
| macs2-treat-pileup-bdg-fastq1 | File | ||
| macs2-treat-pileup-bdg-fastq2 | File | ||
| macs2-peaks-narrow-peak-fastq1 | File | ||
| macs2-peaks-narrow-peak-fastq2 | File | ||
| macs2-control-lambda-bdg-fastq1 | File | ||
| macs2-control-lambda-bdg-fastq2 | File | ||
| samtools-index-bam-index-fastq1 | File | ||
| samtools-index-bam-index-fastq2 | File |
Permalink:
https://w3id.org/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/workflow/epigenome-chip-seq/epigenome-chip-seq.cwl
