From e1a1597ae76322f23a19e87bc8e783d2127a8903 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Fri, 20 Sep 2024 10:24:38 +0100
Subject: [PATCH] Publish the windowmasker outputs too

---
 conf/modules.config | 10 ++++++++++
 docs/output.md      | 16 ++++++++++++++++
 2 files changed, 26 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 1193cf5f..ceeb9c67 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,10 +22,20 @@ process {
 
     withName: "WINDOWMASKER_MKCOUNTS" {
         ext.args = "-infmt fasta -sformat obinary"
+        publishDir = [
+            path: { "${params.outdir}/repeats/windowmasker" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals("versions.yml") ? null : filename.substring(0, filename.length() - 3) + "obinary" }
+        ]
     }
 
     withName: "WINDOWMASKER_USTAT" {
         ext.args = "-infmt fasta -dust T -outfmt fasta"
+        publishDir = [
+            path: { "${params.outdir}/repeats/windowmasker" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
+        ]
     }
 
     withName: "MINIMAP2_HIC" {
diff --git a/docs/output.md b/docs/output.md
index 469f50ad..c9d3222d 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -15,6 +15,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [BlobDir](#blobdir) - Output files viewable on a [BlobToolKit viewer](https://github.com/blobtoolkit/blobtoolkit)
 - [Static plots](#static-plots) - Static versions of the BlobToolKit plots
 - [BUSCO](#busco) - BUSCO results
+- [Repeat masking](#repeat-masking) - Masked repeats (optional)
 - [Read alignments](#read-alignments) - Aligned reads (optional)
 - [Read coverage](#read-coverage) - Read coverage tracks
 - [Base content](#base-content) - _k_-mer statistics (for k &le; 4)
@@ -68,6 +69,21 @@ BUSCO results generated by the pipeline (all BUSCO lineages that match the claas
 
 </details>
 
+### Repeat masking
+
+Reults from the repeat-masker step -- only if the pipeline is run with `--mask`.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `repeats/`
+  - `windowmasker/`
+    - `<accession>.fasta`: masked assembly in Fasta format.
+    - `<accession>.obinary`: frequency counts of repeats, in windowmasker's own binary format.
+
+</details>
+
+
 ### Read alignments
 
 Read alignments in BAM format -- only if the pipeline is run with `--align`.