update doc with skip options

docs/usage.md

@@ -51,6 +51,11 @@
     * [`--splitFastq`](#--splitFastq)
     * [`--saveReference`](#--saveReference)
     * [`--saveAlignedIntermediates`](#--saveAlignedIntermediates)
+* [Skip options](#skip-options)
+  * [--skip_maps](#--skip_maps)
+  * [--skip_ice](#--skip_ice)
+  * [--skip_cool](#--skip_cool)
+  * [--skip_multiqc](#--skip_multiqc)  
 * [Job resources](#job-resources)
 * [Automatic resubmission](#automatic-resubmission)
 * [Custom resource requests](#custom-resource-requests)
@@ -457,6 +462,40 @@ If specified, all intermediate mapping files are saved and exported in the resul
 --saveReference
 ```
 
+## Skip options
+
+#### `--skip_maps`
+
+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
+```
+
+#### `--skip_ice`
+
+If defined, the ICE normalization is not run on the raw contact maps. Default: false
+
+```bash
+--skip_ice
+```
+
+#### `--skip_cool`
+
+If defined, cooler files are not generated. Default: false
+
+```bash
+--skip_cool
+```
+
+#### `--skip_multiqc`
+
+If defined, the MultiQC report is not generated. Default: false
+
+```bash
+--skip_multiqc
+```
+
 ## Job resources
 ### Automatic resubmission
 Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.