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 01/16] 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"

From b35264e9196d8f7c74c28a7bd5bc126a5e16afe8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:11:37 +0200
Subject: [PATCH 02/16] bugfixes

---
 modules/bamtools/split/main.nf       | 6 ++----
 modules/bamtools/split/meta.yml      | 2 +-
 tests/modules/bamtools/split/main.nf | 2 +-
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index f6382d97..2f5ef09f 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -20,7 +20,6 @@ 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) {
@@ -30,9 +29,8 @@ process BAMTOOLS_SPLIT {
     """
     bamtools merge \\
         ${input_list} \\
-        $args \\
-    bamtools split \\
-        $args2
+    | bamtools split \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index 6c534281..0fd5d5ca 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -28,7 +28,7 @@ input:
   - bam_list:
       type: file
       description: |
-        Input file containing bam files to merge before splitting,
+        Optional input file containing bam files to merge before splitting,
         one line per file
 
 output:
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index eb0bed01..9f30c4f9 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -10,5 +10,5 @@ workflow test_bamtools_split {
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT ( input, [] )
 }

From 07982d6cb13649c308625bb3d215c39979e1207c Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:31:39 +0200
Subject: [PATCH 03/16] fix command line, fix meta.yml

---
 modules/bamtools/split/main.nf        | 5 ++++-
 tests/modules/bamtools/split/test.yml | 9 +++++----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 2f5ef09f..f72d13be 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -23,7 +23,10 @@ process BAMTOOLS_SPLIT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
     if (bam_list) {
-        input += " -list $bam_list"
+        input_list += " -list $bam_list"
+    }
+    if (!args.contains("-stub")) {
+        args += " -stub ${prefix}"
     }
 
     """
diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index 4f52e9ce..b52cc9ee 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,10 +1,11 @@
 - name: bamtools split test_bamtools_split
-  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
+  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config
   tags:
-    - bamtools/split
     - bamtools
+    - bamtools/split
   files:
-    - path: output/bamtools/test.paired_end.sorted.REF_chr22.bam
+    - path: output/bamtools/test.REF_chr22.bam
       md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
-    - path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam
+    - path: output/bamtools/test.REF_unmapped.bam
       md5sum: e0754bf72c51543b2d745d96537035fb
+    - path: output/bamtools/versions.yml

From 413980e93a9cb8ba51f430d8a794cb25c43e9305 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:33:16 +0200
Subject: [PATCH 04/16] make use of  dependent on input array size

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

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

From d617a50371abf87bdb376844926088c478ae3f51 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:39:25 +0200
Subject: [PATCH 05/16] add extra test

---
 tests/modules/bamtools/split/main.nf | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index 9f30c4f9..2fc16d67 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -4,11 +4,21 @@ nextflow.enable.dsl = 2
 
 include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
 
-workflow test_bamtools_split {
+workflow test_bamtools_split_single_input {
 
     input = [
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
 
-    BAMTOOLS_SPLIT ( input, [] )
+    BAMTOOLS_SPLIT ( input )
+}
+
+workflow test_bamtools_split_multiple_input {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
+    [
+
+    BAMTOOLS_SPLIT ( input )
 }

From d293cffc6a3beb7f1ef9bab6e95ea421f622b2a5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:42:43 +0200
Subject: [PATCH 06/16] update tests

---
 tests/modules/bamtools/split/main.nf | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index 2fc16d67..ef4b9d59 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -2,15 +2,17 @@
 
 nextflow.enable.dsl = 2
 
-include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE   } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/bamtools/split/main.nf'
 
 workflow test_bamtools_split_single_input {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT_SINGLE ( input )
 }
 
 workflow test_bamtools_split_multiple_input {
@@ -20,5 +22,5 @@ workflow test_bamtools_split_multiple_input {
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
     [
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT_MULTIPLE ( input )
 }

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 07/16] 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

From b4af3f1475b91d0c411e901d6126515babcdafec Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 15:02:41 +0200
Subject: [PATCH 08/16] test fixes

---
 modules/bamtools/split/main.nf       | 9 ++-------
 tests/modules/bamtools/split/main.nf | 9 ++++++---
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index f72d13be..7184261e 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -9,7 +9,6 @@ process BAMTOOLS_SPLIT {
 
     input:
     tuple val(meta), path(bam)
-    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -22,17 +21,13 @@ process BAMTOOLS_SPLIT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
-    if (bam_list) {
-        input_list += " -list $bam_list"
-    }
-    if (!args.contains("-stub")) {
-        args += " -stub ${prefix}"
-    }
+    def stub =  !args.contains("-stub") ? "-stub ${prefix}" : ""
 
     """
     bamtools merge \\
         ${input_list} \\
     | bamtools split \\
+        $stub \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index ef4b9d59..ff0cb748 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -15,12 +15,15 @@ workflow test_bamtools_split_single_input {
     BAMTOOLS_SPLIT_SINGLE ( input )
 }
 
-workflow test_bamtools_split_multiple_input {
+workflow test_bamtools_split_multiple {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
-    [
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]
+
+    ]
 
     BAMTOOLS_SPLIT_MULTIPLE ( input )
 }
+

From 3bcae8e71e705f289ec3786e7b6255eb5e0d56af Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 15:19:52 +0200
Subject: [PATCH 09/16] fix testing errors

---
 tests/modules/bamtools/split/main.nf  |  2 +-
 tests/modules/bamtools/split/test.yml | 16 ++++++++++++++--
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index ff0cb748..9787b4ed 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -20,7 +20,7 @@ workflow test_bamtools_split_multiple {
     input = [
         [ id:'test', single_end:false ], // meta map
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
 
     ]
 
diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index b52cc9ee..63ecac57 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,5 +1,5 @@
-- name: bamtools split test_bamtools_split
-  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config
+- name: bamtools split test_bamtools_split_single_input
+  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_single_input -c tests/config/nextflow.config
   tags:
     - bamtools
     - bamtools/split
@@ -9,3 +9,15 @@
     - path: output/bamtools/test.REF_unmapped.bam
       md5sum: e0754bf72c51543b2d745d96537035fb
     - path: output/bamtools/versions.yml
+
+- name: bamtools split test_bamtools_split_multiple
+  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_multiple -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/split
+  files:
+    - path: output/bamtools/test.REF_chr22.bam
+      md5sum: 585675bea34c48ebe9db06a561d4b4fa
+    - path: output/bamtools/test.REF_unmapped.bam
+      md5sum: 16ad644c87b9471f3026bc87c98b4963
+    - path: output/bamtools/versions.yml

From 2a2ac290c37fbbd6caa41b06993818491131e0f2 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:00 +0200
Subject: [PATCH 10/16] Update modules/bamtools/split/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index 0fd5d5ca..badc6974 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -23,7 +23,7 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: A list of BAM files to merge and then split
+      description: A list of one or more BAM files to merge and then split
       pattern: "*.bam"
   - bam_list:
       type: file

From 7bcede747411d77f85dde0c33e3599e81c0cdb14 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:14 +0200
Subject: [PATCH 11/16] Update modules/bamtools/split/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/meta.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index badc6974..8af701f0 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -25,11 +25,6 @@ input:
       type: file
       description: A list of one or more BAM files to merge and then split
       pattern: "*.bam"
-  - bam_list:
-      type: file
-      description: |
-        Optional input file containing bam files to merge before splitting,
-        one line per file
 
 output:
   - meta:

From b73662c8d9b5a770904ae9f3b1a79c878f125c6c Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:32 +0200
Subject: [PATCH 12/16] Update tests/modules/bamtools/split/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bamtools/split/main.nf | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index 9787b4ed..e5c15c32 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -19,9 +19,10 @@ workflow test_bamtools_split_multiple {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
-
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+        ]
     ]
 
     BAMTOOLS_SPLIT_MULTIPLE ( input )

From 6efb022f6943ff67421b46359b38582a36278fe5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:44 +0200
Subject: [PATCH 13/16] Update tests/modules/bamtools/split/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bamtools/split/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index 63ecac57..5747aa25 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -11,7 +11,7 @@
     - path: output/bamtools/versions.yml
 
 - name: bamtools split test_bamtools_split_multiple
-  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_multiple -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
   tags:
     - bamtools
     - bamtools/split

From e9c44f3d85b731add02680fa6a246c0675e1aac7 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:35:34 +0200
Subject: [PATCH 14/16] Update tests/modules/bamtools/split/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bamtools/split/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index 5747aa25..af639b43 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,5 +1,5 @@
 - name: bamtools split test_bamtools_split_single_input
-  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_single_input -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
   tags:
     - bamtools
     - bamtools/split

From 2d32267fcdce945375294cb776ca129038d2b903 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:36:01 +0200
Subject: [PATCH 15/16] Update modules/bamtools/split/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/main.nf | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 7184261e..9c643b84 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -24,11 +24,13 @@ process BAMTOOLS_SPLIT {
     def stub =  !args.contains("-stub") ? "-stub ${prefix}" : ""
 
     """
-    bamtools merge \\
-        ${input_list} \\
-    | bamtools split \\
-        $stub \\
-        $args
+    bamtools \\
+        merge \\
+        $input_list \\
+        | bamtools \\
+            split \\
+            -stub $prefix \\
+            $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From da56a2d50968f12ff2aa1a6d6b05fae083ba26c3 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:36:08 +0200
Subject: [PATCH 16/16] Update modules/bamtools/split/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 9c643b84..aaa5b663 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -21,8 +21,6 @@ process BAMTOOLS_SPLIT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
-    def stub =  !args.contains("-stub") ? "-stub ${prefix}" : ""
-
     """
     bamtools \\
         merge \\