From 7e883da90460f77b3745468452b4c549327dde13 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:50:50 +0200
Subject: [PATCH] Revert "make use of  dependent on input array size"

This reverts commit 413980e93a9cb8ba51f430d8a794cb25c43e9305.
---
 modules/bamtools/split/main.nf | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 7d69a824..f72d13be 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -9,6 +9,7 @@ process BAMTOOLS_SPLIT {
 
     input:
     tuple val(meta), path(bam)
+    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -20,22 +21,18 @@ process BAMTOOLS_SPLIT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     def input_list = bam.collect{"-in $it"}.join(' ')
-    def stub_cmd = !args.contains("-stub") : " -stub ${prefix}" : ""
-
-    if (size(bam) > 1){
-        def bamtools_merge_cmd = "bamtools merge ${input_list} |"
-    } else {
-        def split_input = input_list
+    if (bam_list) {
+        input_list += " -list $bam_list"
+    }
+    if (!args.contains("-stub")) {
+        args += " -stub ${prefix}"
     }
 
-
     """
-    ${bamtools_merge_cmd} \\
-    bamtools split \\
-        $split_input \\
-        $stub_cmd \\
+    bamtools merge \\
+        ${input_list} \\
+    | bamtools split \\
         $args
 
     cat <<-END_VERSIONS > versions.yml