From e55ab8a33cdc6dae24e86148bdfde49411eb9461 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 6 Feb 2024 09:38:43 +0100
Subject: [PATCH] add iterative and cutsite options to docs

---
 README.md              |  2 +-
 conf/modules.config    |  5 +++++
 docs/hicstuff_usage.md | 48 ++++++++++++++++++++++++++++++++++++++++--
 docs/usage.md          | 31 +++++++++++++++++++++++++++
 4 files changed, 83 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 1deba86..d0c91f0 100644
--- a/README.md
+++ b/README.md
@@ -68,7 +68,7 @@ nextflow run main.nf \
 ```
 If your not running the pipeline on the PSMN, make sure you have Docker installed and use `-profile docker` instead.
 
-For detailed options, please refer to the [parameter documentation](docs/usage.md).
+For detailed options, please refer to the parameter documentation for [hicpro](docs/usage.md) or [hicstuff](docs/hicstuff_usage.md).
 
 ## Pipeline output
 
diff --git a/conf/modules.config b/conf/modules.config
index e2f6984..ac70e5d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -461,5 +461,10 @@ process {
             " -l ${params.hicstuff_read_len}"
             ].join('').trim()
         }
+        publishDir = [
+            path: { "${params.outdir}/iteralign" },
+            mode: 'copy',
+            enabled: params.save_bam
+        ]
     }
 }
diff --git a/docs/hicstuff_usage.md b/docs/hicstuff_usage.md
index aaf46ee..c084b0c 100644
--- a/docs/hicstuff_usage.md
+++ b/docs/hicstuff_usage.md
@@ -107,6 +107,39 @@ If not specified, this file will be automatically created by the pipeline.
 In this case, the `--fasta` reference genome will be used.
 Note that the `--digestion` or `--restriction_site` parameter is mandatory to create this file.
 
+
+## Digestion of the reads
+
+### `--cutsite`
+
+Generates new gzipped fastq files from original fastq. The function will cut the reads at their religation sites and creates new pairs of reads with the different fragments obtained after cutting at the digestion sites.
+Default: false
+
+```bash
+--cutsite
+```
+
+> :warning: **Warning**: This option cannot be used at the same time as the iterative mapping.
+
+### `--cutsite_mode`
+
+Mode to use to make the digestion. Three values possible: "all", "for_vs_rev", "pile".
+Default: for_vs_rev
+
+```bash
+--cutsite_mode '[all | for_vs_rev | pile]'
+```
+
+### `--cutsite_seed`
+
+Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)
+Default: 0
+
+```bash
+--cutsite_seed '[Size of fragment]'
+```
+
+
 ## Hicstuff specific parameters
 
 The following options are defined in the `nextflow.config` file, and can be
@@ -117,16 +150,27 @@ command line parameters.
 
 #### `--hicstuff_bwt2_align_opts`
 
-Bowtie2 alignment option for end-to-end mapping.
+Bowtie2 alignment option for normal mode end-to-end mapping.
 Default: '--very-sensitive-local'
 
 ```bash
 --hicstuff_bwt2_align_opts '[Options for bowtie2 mapping on full reads]'
 ```
 
+#### `--iteralign`
+
+Truncate reads from a fastq file to 20 basepairs and iteratively extend and re-align the unmapped reads to optimize the proportion of uniquely aligned reads in a 3C library.
+Default: false
+
+```
+--iteralign
+```
+
+Use [`--hicstuff_min_qual`](#hicstuff_min_qual) to set the minimum quality for the iterative alignment.
+
 #### `--save_bam`
 
-If specified, save BAM files after mapping. Default: false
+If specified, save BAM files after mapping (works for normal and iterative mode). Default: false
 
 ```bash
 --save_bam
diff --git a/docs/usage.md b/docs/usage.md
index 0c3e0f9..cee5e9d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -489,6 +489,37 @@ normalization. Default: 0.1
 --ice_eps '[numeric]'
 ```
 
+## Digestion of the reads
+
+### `--cutsite`
+
+Generates new gzipped fastq files from original fastq. The function will cut the reads at their religation sites and creates new pairs of reads with the different fragments obtained after cutting at the digestion sites.
+Default: false
+
+```bash
+--cutsite
+```
+
+> :warning: **Warning**: This option cannot be used at the same time as the iterative mapping.
+
+### `--cutsite_mode`
+
+Mode to use to make the digestion. Three values possible: "all", "for_vs_rev", "pile".
+Default: for_vs_rev
+
+```bash
+--cutsite_mode '[all | for_vs_rev | pile]'
+```
+
+### `--cutsite_seed`
+
+Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)
+Default: 0
+
+```bash
+--cutsite_seed '[Size of fragment]'
+```
+
 ## Downstream analysis
 
 ### Additional quality controls
-- 
GitLab