Update gzrt to v0.9.1

modules/nf-core/gzrt/environment.yml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::gzrt=0.8"
+  - "bioconda::gzrt=0.9.1"

modules/nf-core/gzrt/main.nf

@@ -4,15 +4,15 @@ process GZRT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gzrt:0.8--he4a0461_0':
-        'biocontainers/gzrt:0.8--he4a0461_0' }"
+        'https://depot.galaxyproject.org/singularity/gzrt:0.9.1--h577a1d6_0':
+        'biocontainers/gzrt:0.9.1--h577a1d6_0' }"
 
     input:
     tuple val(meta), path(fastqgz)
 
     output:
-    tuple val(meta), path("*_recovered.fastq.gz"), emit: fastqrecovered
-    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
@@ -22,10 +22,10 @@ process GZRT {
         error "GZRT works with .gz files only."
     }
 
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_recovered"
+    if ("${fastqgz}" == "${prefix}.fastq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    gzrecover -o ${prefix}_recovered.fastq ${fastqgz}
-    gzip ${prefix}_recovered.fastq
+    gzrecover -p ${fastqgz} | gzip > ${prefix}.fastq.gz
 
     soft_line="${task.process}"
     ver_line="gzrt: \$(gzrecover -V |& sed '1!d ; s/gzrecover //')"
@@ -36,9 +36,10 @@ process GZRT {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_recovered"
+    if ("${fastqgz}" == "${prefix}.fastq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    echo "" | gzip > ${prefix}_recovered.fastq.gz
+    echo "" | gzip > ${prefix}.fastq.gz
 
     soft_line="${task.process}"
     ver_line="gzrt: \$(gzrecover -V |& sed '1!d ; s/gzrecover //')"

modules/nf-core/gzrt/meta.yml

@@ -29,13 +29,13 @@ input:
           - edam: "http://edamontology.org/format_3989"
 
 output:
-  - fastqrecovered:
+  - recovered:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*_recovered.fastq.gz":
+      - "${prefix}.fastq.gz":
           type: file
           description: Recovered FASTQ.gz file
           pattern: "*.{gz}"