From d5d785b3d8b422cda9c6d84a23f629a8e9ff8cd8 Mon Sep 17 00:00:00 2001
From: Benedetto Polimeni <34317613+bepoli@users.noreply.github.com>
Date: Tue, 20 Sep 2022 22:08:29 +0200
Subject: [PATCH] [samtools] add optional csi output (#2064)

* [samtools] add optional csi output, when applicable

* Remove empty line

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
---
 modules/samtools/merge/main.nf  | 2 ++
 modules/samtools/merge/meta.yml | 4 ++++
 modules/samtools/sort/main.nf   | 1 +
 modules/samtools/sort/meta.yml  | 4 ++++
 modules/samtools/view/main.nf   | 1 +
 modules/samtools/view/meta.yml  | 4 ++++
 6 files changed, 16 insertions(+)

diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf
index d01bbed8..6b105382 100644
--- a/modules/samtools/merge/main.nf
+++ b/modules/samtools/merge/main.nf
@@ -15,8 +15,10 @@ process SAMTOOLS_MERGE {
     output:
     tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
     tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
+    tuple val(meta), path("*.csi")         , optional:true, emit: csi
     path  "versions.yml"                                  , emit: versions
 
+
     when:
     task.ext.when == null || task.ext.when
 
diff --git a/modules/samtools/merge/meta.yml b/modules/samtools/merge/meta.yml
index f6833d0c..5bd84bc5 100644
--- a/modules/samtools/merge/meta.yml
+++ b/modules/samtools/merge/meta.yml
@@ -51,6 +51,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - csi:
+      type: file
+      description: BAM index file (optional)
+      pattern: "*.csi"
 authors:
   - "@drpatelh"
   - "@yuukiiwa "
diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf
index b4fc1cbe..ab7f1cca 100644
--- a/modules/samtools/sort/main.nf
+++ b/modules/samtools/sort/main.nf
@@ -12,6 +12,7 @@ process SAMTOOLS_SORT {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.csi"), emit: csi, optional: true
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/samtools/sort/meta.yml b/modules/samtools/sort/meta.yml
index a820c55a..09289751 100644
--- a/modules/samtools/sort/meta.yml
+++ b/modules/samtools/sort/meta.yml
@@ -39,6 +39,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - csi:
+      type: file
+      description: BAM index file (optional)
+      pattern: "*.csi"
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf
index 59ded5c3..83613dd5 100644
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@@ -14,6 +14,7 @@ process SAMTOOLS_VIEW {
     output:
     tuple val(meta), path("*.bam") , emit: bam , optional: true
     tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.csi") , emit: csi,  optional: true
     path  "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/samtools/view/meta.yml b/modules/samtools/view/meta.yml
index a8b43ecc..e32f9b0e 100644
--- a/modules/samtools/view/meta.yml
+++ b/modules/samtools/view/meta.yml
@@ -51,6 +51,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - csi:
+      type: file
+      description: BAM index file (optional)
+      pattern: "*.csi"
 authors:
   - "@drpatelh"
   - "@joseespinosa"