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Commit 3273c92c authored by nservant's avatar nservant
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update skip options

parent f54bf1e1
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......@@ -29,5 +29,5 @@ params {
min_mapq = 0
// Options
skip_cool = true
skipCool = true
}
......@@ -53,10 +53,10 @@
* [`--saveAlignedIntermediates`](#--saveAlignedIntermediates)
* [`--saveInteractionBAM`](#--saveInteractionBAM)
* [Skip options](#skip-options)
* [--skip_maps](#--skip_maps)
* [--skip_ice](#--skip_ice)
* [--skip_cool](#--skip_cool)
* [--skip_multiqc](#--skip_multiqc)
* [--skipMaps](#--skipMaps)
* [--skipIce](#--skipIce)
* [--skipCool](#--skipCool)
* [--skipMultiQC](#--skipMultiQC)
* [Job resources](#job-resources)
* [Automatic resubmission](#automatic-resubmission)
* [Custom resource requests](#custom-resource-requests)
......@@ -561,38 +561,38 @@ dangling end, self-circle, etc.) and its tags.
## Skip options
### `--skip_maps`
### `--skipMaps`
If defined, the workflow stops with the list of valid interactions, and the
genome-wide maps are not built. Usefult for capture-C analysis. Default: false
```bash
--skip_maps
--skipMaps
```
### `--skip_ice`
### `--skipIce`
If defined, the ICE normalization is not run on the raw contact maps.
Default: false
```bash
--skip_ice
--skipIce
```
### `--skip_cool`
### `--skipCool`
If defined, cooler files are not generated. Default: false
```bash
--skip_cool
--skipCool
```
### `--skip_multiqc`
### `--skipMultiQC`
If defined, the MultiQC report is not generated. Default: false
```bash
--skip_multiqc
--skipMultiQC
```
## Job resources
......
......@@ -64,10 +64,10 @@ def helpMessage() {
Workflow
--skip_maps Skip generation of contact maps. Useful for capture-C. Default: False
--skip_ice Skip ICE normalization. Default: False
--skip_cool Skip generation of cool files. Default: False
--skip_multiQC Skip MultiQC. Default: False
--skipMaps Skip generation of contact maps. Useful for capture-C. Default: False
--skipIce Skip ICE normalization. Default: False
--skipCool Skip generation of cool files. Default: False
--skipMultiQC Skip MultiQC. Default: False
Other
--splitFastq Size of read chuncks to use to speed up the workflow. Default: None
......@@ -734,7 +734,7 @@ process build_contact_maps{
publishDir "${params.outdir}/hic_results/matrix/raw", mode: 'copy'
when:
!params.skip_maps
!params.skipMaps
input:
set val(sample), file(vpairs), val(mres) from all_valid_pairs.combine(map_res)
......@@ -759,7 +759,7 @@ process run_ice{
publishDir "${params.outdir}/hic_results/matrix/iced", mode: 'copy'
when:
!params.skip_maps && !params.skip_ice
!params.skipMaps && !params.skipIce
input:
file(rmaps) from raw_maps
......@@ -787,7 +787,7 @@ process generate_cool{
publishDir "${params.outdir}/export/cool", mode: 'copy'
when:
!params.skip_cool
!params.skipCool
input:
set val(sample), file(vpairs) from all_valid_pairs_4cool
......@@ -810,7 +810,7 @@ process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy'
when:
!params.skip_multiqc
!params.skipMultiQC
input:
file multiqc_config from ch_multiqc_config
......
......@@ -16,10 +16,10 @@ params {
readPaths = false
chromosome_size = false
restriction_fragments = false
skip_maps = false
skip_ice = false
skip_cool = false
skip_multiqc = false
skipMaps = false
skipIce = false
skipCool = false
skipMultiQC = false
dnase = false
// Boilerplate options
......
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