From 0f7c04647747f535c94f63908bdd82c77f9a9ed1 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 13 Apr 2022 12:51:17 +0200
Subject: [PATCH 1/9] first commit

---
 modules/elprep/merge/main.nf               | 44 ++++++++++++++++++++++
 modules/elprep/merge/meta.yml              | 44 ++++++++++++++++++++++
 tests/config/pytest_modules.yml            |  4 ++
 tests/modules/elprep/merge/main.nf         | 17 +++++++++
 tests/modules/elprep/merge/nextflow.config |  5 +++
 tests/modules/elprep/merge/test.yml        | 11 ++++++
 6 files changed, 125 insertions(+)
 create mode 100644 modules/elprep/merge/main.nf
 create mode 100644 modules/elprep/merge/meta.yml
 create mode 100644 tests/modules/elprep/merge/main.nf
 create mode 100644 tests/modules/elprep/merge/nextflow.config
 create mode 100644 tests/modules/elprep/merge/test.yml

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
new file mode 100644
index 00000000..8312d35b
--- /dev/null
+++ b/modules/elprep/merge/main.nf
@@ -0,0 +1,44 @@
+process ELPREP_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
+        'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("**.{bam,sam}"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        args += " --single-end"
+    }
+    def suffix = args.contains("--output-type sam") ? "sam" : "bam"
+
+    """
+    # create directory and move all input so elprep can find and merge them before splitting
+    mkdir input
+    mv ${bam} input/
+
+    elprep merge \\
+        input \\
+        ${prefix}.${suffix} \\
+        $args \\
+        --nr-of-threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/elprep/merge/meta.yml b/modules/elprep/merge/meta.yml
new file mode 100644
index 00000000..e157fddb
--- /dev/null
+++ b/modules/elprep/merge/meta.yml
@@ -0,0 +1,44 @@
+name: "elprep_merge"
+description: Merge split bam/sam chunks in one file
+keywords:
+  - bam
+  - sam
+  - merge
+tools:
+  - "elprep":
+      description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      doi: ""
+      licence: "['AGPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: List of BAM/SAM chunks to merge
+      pattern: "*.{bam,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  #
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - bam:
+      type: file
+      description: Merged BAM/SAM file
+      pattern: "*.{bam,sam}"
+
+authors:
+  - "@matthdsm"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index cd4913cf..ea22a0d6 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -587,6 +587,10 @@ ectyper:
   - modules/ectyper/**
   - tests/modules/ectyper/**
 
+elprep/merge:
+  - modules/elprep/merge/**
+  - tests/modules/elprep/merge/**
+
 emmtyper:
   - modules/emmtyper/**
   - tests/modules/emmtyper/**
diff --git a/tests/modules/elprep/merge/main.nf b/tests/modules/elprep/merge/main.nf
new file mode 100644
index 00000000..b4a40ce3
--- /dev/null
+++ b/tests/modules/elprep/merge/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
+include { ELPREP_MERGE } from '../../../../modules/elprep/merge/main.nf'
+
+workflow test_elprep_merge {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    ELPREP_SPLIT ( input )
+    ELPREP_MERGE ( ELPREP_SPLIT.out.bam )
+}
diff --git a/tests/modules/elprep/merge/nextflow.config b/tests/modules/elprep/merge/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/elprep/merge/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
new file mode 100644
index 00000000..c66fe030
--- /dev/null
+++ b/tests/modules/elprep/merge/test.yml
@@ -0,0 +1,11 @@
+- name: "elprep merge"
+  command: nextflow run ./tests/modules/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config -c ./tests/modules/elprep/merge/nextflow.config
+  tags:
+    - "elprep"
+    #
+    - "elprep/merge"
+    #
+  files:
+    - path: "output/elprep/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/elprep/versions.yml

From ccef7f857917189fe1c2563c4d68deb038bade4b Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 11:26:01 +0200
Subject: [PATCH 2/9] alignment

---
 modules/elprep/merge/main.nf        | 4 ++--
 tests/modules/elprep/merge/test.yml | 3 ---
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 8312d35b..010156f2 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -11,8 +11,8 @@ process ELPREP_MERGE {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("**.{bam,sam}"), emit: bam
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("**.{bam,sam}")   , emit: bam
+    path "versions.yml"                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
index c66fe030..26c16f59 100644
--- a/tests/modules/elprep/merge/test.yml
+++ b/tests/modules/elprep/merge/test.yml
@@ -2,10 +2,7 @@
   command: nextflow run ./tests/modules/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config -c ./tests/modules/elprep/merge/nextflow.config
   tags:
     - "elprep"
-    #
     - "elprep/merge"
-    #
   files:
     - path: "output/elprep/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
     - path: output/elprep/versions.yml

From ad15d1b7922c8de1b4b84897e4a44182f5b52299 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 11:27:55 +0200
Subject: [PATCH 3/9] update label

---
 modules/elprep/merge/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 010156f2..00ed4d60 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -1,6 +1,6 @@
 process ELPREP_MERGE {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
 
     conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

From 8dad38afc7f28db49c38a23deb7abfeca2ee3bc7 Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 11:35:14 +0200
Subject: [PATCH 4/9] fix test.yml

---
 tests/modules/elprep/merge/test.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
index 26c16f59..d6037bec 100644
--- a/tests/modules/elprep/merge/test.yml
+++ b/tests/modules/elprep/merge/test.yml
@@ -1,8 +1,8 @@
-- name: "elprep merge"
-  command: nextflow run ./tests/modules/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config -c ./tests/modules/elprep/merge/nextflow.config
+- name: elprep merge test_elprep_merge
+  command: nextflow run tests/modules/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config
   tags:
-    - "elprep"
-    - "elprep/merge"
+    - elprep
+    - elprep/merge
   files:
-    - path: "output/elprep/test.bam"
+    - path: output/elprep/test.bam
     - path: output/elprep/versions.yml

From c4072f274cdf91601c895b206f2011e0b4b809df Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:39:22 +0200
Subject: [PATCH 5/9] fix formatting, fix code style

---
 modules/elprep/merge/main.nf | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 00ed4d60..2b12bfe2 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -18,12 +18,10 @@ process ELPREP_MERGE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        args += " --single-end"
-    }
-    def suffix = args.contains("--output-type sam") ? "sam" : "bam"
+    def args        = task.ext.args ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def suffix      = args.contains("--output-type sam") ? "sam" : "bam"
+    def single_end  = meta.single_end ? " --single-end" : ""
 
     """
     # create directory and move all input so elprep can find and merge them before splitting
@@ -34,6 +32,7 @@ process ELPREP_MERGE {
         input \\
         ${prefix}.${suffix} \\
         $args \\
+        ${single_end} \\
         --nr-of-threads $task.cpus
 
     cat <<-END_VERSIONS > versions.yml

From 2f6382168cac2ca8a9ff9d53c868fbde1a0ca5e1 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:51:54 +0200
Subject: [PATCH 6/9] update meta.yml

---
 modules/elprep/merge/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/elprep/merge/meta.yml b/modules/elprep/merge/meta.yml
index e157fddb..1f49b1a0 100644
--- a/modules/elprep/merge/meta.yml
+++ b/modules/elprep/merge/meta.yml
@@ -7,10 +7,10 @@ keywords:
 tools:
   - "elprep":
       description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
-      homepage: "None"
-      documentation: "None"
-      tool_dev_url: "None"
-      doi: ""
+      homepage: "https://github.com/ExaScience/elprep"
+      documentation: "https://github.com/ExaScience/elprep"
+      tool_dev_url: "https://github.com/ExaScience/elprep"
+      doi: "10.1371/journal.pone.0244471"
       licence: "['AGPL v3']"
 
 input:

From fefffb9bb0776e679c2297e8d80325d57e2f2d7a Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 12:36:32 +0200
Subject: [PATCH 7/9] fix output glob

---
 modules/elprep/merge/main.nf        | 6 +++---
 tests/modules/elprep/merge/test.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 2b12bfe2..28fa9985 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -11,8 +11,8 @@ process ELPREP_MERGE {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("**.{bam,sam}")   , emit: bam
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("output/**.{bam,sam}")    , emit: bam
+    path "versions.yml"                             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,7 +30,7 @@ process ELPREP_MERGE {
 
     elprep merge \\
         input \\
-        ${prefix}.${suffix} \\
+        output/${prefix}.${suffix} \\
         $args \\
         ${single_end} \\
         --nr-of-threads $task.cpus
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
index d6037bec..ad2ecfef 100644
--- a/tests/modules/elprep/merge/test.yml
+++ b/tests/modules/elprep/merge/test.yml
@@ -4,5 +4,5 @@
     - elprep
     - elprep/merge
   files:
-    - path: output/elprep/test.bam
+    - path: output/elprep/output/test.bam
     - path: output/elprep/versions.yml

From 9a2dad935cad22789380f94b67a44181e89e4392 Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 13:13:39 +0200
Subject: [PATCH 8/9] update config

---
 tests/modules/elprep/merge/nextflow.config | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/modules/elprep/merge/nextflow.config b/tests/modules/elprep/merge/nextflow.config
index 50f50a7a..4e4570f4 100644
--- a/tests/modules/elprep/merge/nextflow.config
+++ b/tests/modules/elprep/merge/nextflow.config
@@ -1,5 +1,5 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
+    withName : ELPREP_MERGE {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+}

From 9d0f03d96a6855af87f19f27728757e839e51842 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 15:07:09 +0200
Subject: [PATCH 9/9] Update modules/elprep/merge/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/elprep/merge/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 28fa9985..d5ffc497 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -29,7 +29,7 @@ process ELPREP_MERGE {
     mv ${bam} input/
 
     elprep merge \\
-        input \\
+        input/ \\
         output/${prefix}.${suffix} \\
         $args \\
         ${single_end} \\