update skip options

conf/test.config

@@ -29,5 +29,5 @@ params {
   min_mapq = 0
 
   // Options
-  skip_cool = true
+  skipCool = true
 }

docs/usage.md

@@ -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

main.nf

@@ -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

nextflow.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