update usage readme with saving options

docs/README.md

-# nf-core/hic: Documentation
+# Meta HiC pipeline: Documentation
 
-The nf-core/hic documentation is split into the following pages:
+The Meta HiC pipeline is split into the following pages:
 
-- [Usage](usage.md)
-  - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
+- [Usage hicpro workflow](usage.md)
+  - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicpro workflow.
+- [Usage hicstuff workflow](hicstuff_usage.md)
+  - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicstuff workflow.
 - [Output](output.md)
-  - An overview of the different results produced by the pipeline and how to interpret them.
+  - /!\TO UPDATE/!\ An overview of the different results produced by the pipeline and how to interpret them.
 
 You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)

docs/hicstuff_usage.md

@@ -124,6 +124,14 @@ Default: '--very-sensitive-local'
 --hicstuff_bwt2_align_opts '[Options for bowtie2 mapping on full reads]'
 ```
 
+#### `--save_bam`
+
+If specified, save BAM files after mapping. Default: false
+
+```bash
+--save_bam
+```
+
 ### Fragment enzyme
 
 #### `--hicstuff_min_size`
@@ -168,6 +176,14 @@ Name of fragments plot file. Default: 'frags_hist.pdf'
 --hicstuff_frags_plot_path '[Name of fragments plot file]'
 ```
 
+#### `--save_fragments`
+
+If specified, save fragments file. Default: false
+
+```bash
+--save_fragments
+```
+
 ### Bam2pairs
 
 #### `--hicstuff_valid_pairs`
@@ -193,6 +209,15 @@ Minimum mapping quality required to keep a pair of Hi-C reads. Default:30
 
 [#### `--hicstuff_circular`](#hicstuff_circular)
 
+#### `--save_pairs`
+
+If specified, save pair files. Default: false
+
+```bash
+--save_pairs
+```
+
+
 ### Matrix
 
 #### `--hicstuff_matrix`
@@ -324,3 +349,11 @@ If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If
 --filter_pcr_picard
 ```
 
+#### `--save_bam_intermediates`
+
+If specified, save BAM files after PICARD pcr filtering. Default: false
+
+```bash
+--save_bam_intermediates
+```
+

docs/usage.md

@@ -400,6 +400,22 @@ Note that in this case the `--min_mapq` parameter is ignored.
 --keep_multi
 ```
 
+#### `--save_bam_intermediates`
+
+If specified, save BAM files after PICARD pcr filtering. Default: false
+
+```bash
+--save_bam_intermediates
+```
+
+#### `--save_pairs`
+
+If specified, save pair files. Default: false
+
+```bash
+--save_pairs
+```
+
 ## Genome-wide contact maps
 
 Once the list of valid pairs is available, the standard is now to move on the `cooler`
@@ -555,6 +571,14 @@ results folder. Default: false
 --save_aligned_inermediates
 ```
 
+### `--save_bam`
+
+If specified, save BAM files after mapping. Default: false
+
+```bash
+--save_bam
+```
+
 ### `--save_interaction_bam`
 
 If specified, write a BAM file with all classified reads (valid pairs,

nextflow_schema.json

@@ -231,7 +231,7 @@
                 },
                 "save_bam_intermediates": {
                     "type": "boolean",
-                    "description": "Save  BAM files PICARD pcr duplicates filtering"
+                    "description": "Save BAM files PICARD pcr duplicates filtering"
                 },
                 "save_pairs": {
                     "type": "boolean",