From e87b963ea90e68e85bfb113f6ba5e656ad77907b Mon Sep 17 00:00:00 2001
From: Tommaso Mazza <t.mazza@operapadrepio.it>
Date: Mon, 23 Dec 2024 19:09:07 +0000
Subject: [PATCH] Add args in command line - gzrt

---
 modules/nf-core/gzrt/main.nf                 | 13 +--
 modules/nf-core/gzrt/tests/main.nf.test.snap | 89 ++++++++++----------
 2 files changed, 52 insertions(+), 50 deletions(-)

diff --git a/modules/nf-core/gzrt/main.nf b/modules/nf-core/gzrt/main.nf
index 2205b4251de..a8c398ec652 100644
--- a/modules/nf-core/gzrt/main.nf
+++ b/modules/nf-core/gzrt/main.nf
@@ -11,14 +11,15 @@ process GZRT {
     tuple val(meta), path(fastqgz)
 
     output:
-    tuple val(meta), path("${prefix}(?:_1|_2)?.fastq.gz"), emit: recovered
-    path "versions.yml"                                  , emit: versions
+    tuple val(meta), path("${prefix}*.fastq.gz"), emit: recovered
+    path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    prefix = task.ext.prefix ?: "${meta.id}_recovered"
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}_recovered"
     fastqgz.each { file ->
         if (file.extension != "gz") {
             error "GZRT works with .gz files only. Offending file: ${file}"
@@ -32,14 +33,14 @@ process GZRT {
 
     """
     if [ "$meta.single_end" == true ]; then
-        gzrecover -p ${fastqgz} | gzip > ${prefix}.fastq.gz
+        gzrecover ${args} -p ${fastqgz} | gzip > ${prefix}.fastq.gz
 
         if [ -e "${prefix}.fastq.gz" ] && [ ! -s "${prefix}.fastq.gz" ]; then
             echo "" | gzip > ${prefix}.fastq.gz
         fi
     else
-        gzrecover -p ${fastqgz[0]} | gzip > ${prefix}_1.fastq.gz
-        gzrecover -p ${fastqgz[1]} | gzip > ${prefix}_2.fastq.gz
+        gzrecover ${args} -p ${fastqgz[0]} | gzip > ${prefix}_1.fastq.gz
+        gzrecover ${args} -p ${fastqgz[1]} | gzip > ${prefix}_2.fastq.gz
 
         if [ -e "${prefix}_1.fastq.gz" ] && [ ! -s "${prefix}_1.fastq.gz" ]; then
             echo "" | gzip > ${prefix}_1.fastq.gz
diff --git a/modules/nf-core/gzrt/tests/main.nf.test.snap b/modules/nf-core/gzrt/tests/main.nf.test.snap
index 2a574165110..af87aac1011 100644
--- a/modules/nf-core/gzrt/tests/main.nf.test.snap
+++ b/modules/nf-core/gzrt/tests/main.nf.test.snap
@@ -1,14 +1,14 @@
 {
-    "Run gzrt on test2_1_corrupted - fastq.gz - stub": {
+    "Run gzrt on test2_1_corrupted single-end - fastq.gz": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test-single",
+                            "single_end": true
                         },
-                        "test_recovered.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test-single_recovered.fastq.gz:md5,78b566f63fbd4e4c29902c6217993e03"
                     ]
                 ],
                 "1": [
@@ -17,10 +17,10 @@
                 "recovered": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test-single",
+                            "single_end": true
                         },
-                        "test_recovered.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test-single_recovered.fastq.gz:md5,78b566f63fbd4e4c29902c6217993e03"
                     ]
                 ],
                 "versions": [
@@ -32,18 +32,21 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-22T10:35:18.233218"
+        "timestamp": "2024-12-23T19:00:33.679803153"
     },
-    "Run gzrt on test2_1_corrupted single-end - fastq.gz": {
+    "Run gzrt on test2_1_corrupted - fastq.gz - stub": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test-single",
-                            "single_end": true
+                            "id": "test",
+                            "single_end": false
                         },
-                        "test-single_recovered.fastq.gz:md5,78b566f63fbd4e4c29902c6217993e03"
+                        [
+                            "test_recovered_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_recovered_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
                     ]
                 ],
                 "1": [
@@ -52,10 +55,13 @@
                 "recovered": [
                     [
                         {
-                            "id": "test-single",
-                            "single_end": true
+                            "id": "test",
+                            "single_end": false
                         },
-                        "test-single_recovered.fastq.gz:md5,78b566f63fbd4e4c29902c6217993e03"
+                        [
+                            "test_recovered_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_recovered_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
                     ]
                 ],
                 "versions": [
@@ -67,45 +73,40 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-22T14:48:19.882831"
+        "timestamp": "2024-12-23T19:01:25.657233606"
     },
     "Run gzrt on test2_1_corrupted paired-end - fastq.gz": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "recovered": [
-                    
-                ],
-                "versions": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2024-12-22T14:49:18.818601"
-    },
-    "Run gzrt on test2_1_corrupted - fastq.gz": {
-        "content": [
-            {
-                "0": [
-                    
+                    [
+                        {
+                            "id": "test-paired",
+                            "single_end": false
+                        },
+                        [
+                            "test-paired_recovered_1.fastq.gz:md5,78b566f63fbd4e4c29902c6217993e03",
+                            "test-paired_recovered_2.fastq.gz:md5,641919946a0e572ca7483f6e54476f3b"
+                        ]
+                    ]
                 ],
                 "1": [
-                    
+                    "versions.yml:md5,6d1e28b8a8043e3cba67606c7acdc676"
                 ],
                 "recovered": [
-                    
+                    [
+                        {
+                            "id": "test-paired",
+                            "single_end": false
+                        },
+                        [
+                            "test-paired_recovered_1.fastq.gz:md5,78b566f63fbd4e4c29902c6217993e03",
+                            "test-paired_recovered_2.fastq.gz:md5,641919946a0e572ca7483f6e54476f3b"
+                        ]
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,6d1e28b8a8043e3cba67606c7acdc676"
                 ]
             }
         ],
@@ -113,6 +114,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-22T14:35:45.10345"
+        "timestamp": "2024-12-23T19:01:02.506192477"
     }
 }
\ No newline at end of file