From 6723ca7f9068ecbdee31dcad07f3115dc5b40667 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:05:02 +0200
Subject: [PATCH] bump version, add merge before split

---
 modules/bamtools/split/main.nf  | 22 +++++++++++++++-------
 modules/bamtools/split/meta.yml |  8 +++++++-
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 014e5cdb..f6382d97 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -2,13 +2,14 @@ process BAMTOOLS_SPLIT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
-        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
+        'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
 
     input:
     tuple val(meta), path(bam)
+    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -19,12 +20,19 @@ process BAMTOOLS_SPLIT {
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_list = bam.collect{"-in $it"}.join(' ')
+    if (bam_list) {
+        input += " -list $bam_list"
+    }
+
     """
-    bamtools \\
-        split \\
-        -in $bam \\
-        $args
+    bamtools merge \\
+        ${input_list} \\
+        $args \\
+    bamtools split \\
+        $args2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index 0e848212..6c534281 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -23,8 +23,13 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: A BAM file to split
+      description: A list of BAM files to merge and then split
       pattern: "*.bam"
+  - bam_list:
+      type: file
+      description: |
+        Input file containing bam files to merge before splitting,
+        one line per file
 
 output:
   - meta:
@@ -43,3 +48,4 @@ output:
 
 authors:
   - "@sguizard"
+  - "@matthdsm"