Update CENTRIFUGE: bump versions, fix missing args, and command forma…

…tting (#7205) * bump versions and fix missing args and command formatting * CI: docker self hosted - userEmulate and dont fixOwnership * try suggestion from claude * fix cgroup parent slice * rm cgroup parent slice * rm security opts * userns n security opts * Update tests/config/nf-test.config --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Sateesh <perisateesh@gmail.com>
nf-core · Dec 19, 2024 · 8581a56 · 8581a56
1 parent ce1a665
commit 8581a56
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Showing 8 changed files with 57 additions and 47 deletions.
diff --git a/modules/nf-core/centrifuge/build/environment.yml b/modules/nf-core/centrifuge/build/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/build/main.nf b/modules/nf-core/centrifuge/build/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_BUILD {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(fasta)
@@ -15,8 +15,8 @@ process CENTRIFUGE_BUILD {
     path size_table
 
     output:
-    tuple val(meta), path("${prefix}/") , emit: cf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${prefix}/"), emit: cf
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,13 +29,15 @@ process CENTRIFUGE_BUILD {
     mkdir ${prefix}
 
     centrifuge-build \\
-        -p $task.cpus \\
-        $fasta \\
+        -p ${task.cpus} \\
+        ${fasta} \\
         ${prefix}/${prefix} \\
-        --conversion-table $conversion_table \\
-        --taxonomy-tree $taxonomy_tree \\
-        --name-table $name_table \\
-        ${size_table_cmd}
+        --conversion-table ${conversion_table} \\
+        --taxonomy-tree ${taxonomy_tree} \\
+        --name-table ${name_table} \\
+        ${size_table_cmd} \\
+        ${args} \\
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,7 +46,7 @@ process CENTRIFUGE_BUILD {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p ${prefix}/

diff --git a/modules/nf-core/centrifuge/build/tests/main.nf.test.snap b/modules/nf-core/centrifuge/build/tests/main.nf.test.snap
@@ -80,9 +80,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-02-15T10:10:19.439629103"
+        "timestamp": "2024-12-12T10:38:44.613715625"
     }
 }
diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_CENTRIFUGE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(reads)
@@ -14,26 +14,27 @@ process CENTRIFUGE_CENTRIFUGE {
     val save_aligned
 
     output:
-    tuple val(meta), path('*report.txt')                 , emit: report
-    tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.{sam,tab}')                 , optional: true, emit: sam
-    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
-    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
-    path "versions.yml"                                  , emit: versions
+    tuple val(meta), path('*report.txt'), emit: report
+    tuple val(meta), path('*results.txt'), emit: results
+    tuple val(meta), path('*.{sam,tab}'), optional: true, emit: sam
+    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_mapped
+    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_unmapped
+    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}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
@@ -49,13 +50,13 @@ process CENTRIFUGE_CENTRIFUGE {
     centrifuge \\
         -x \$db_name \\
         --temp-directory ./temp \\
-        -p $task.cpus \\
-        $paired \\
+        -p ${task.cpus} \\
+        ${paired} \\
         --report-file ${prefix}.report.txt \\
         -S ${prefix}.results.txt \\
-        $unaligned \\
-        $aligned \\
-        $args
+        ${unaligned} \\
+        ${aligned} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -64,15 +65,16 @@ process CENTRIFUGE_CENTRIFUGE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def _paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }

diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf
@@ -1,19 +1,19 @@
 process CENTRIFUGE_KREPORT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(report)
     path db
 
     output:
     tuple val(meta), path('*.txt'), emit: kreport
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,7 +23,10 @@ process CENTRIFUGE_KREPORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
-    centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
+    centrifuge-kreport \\
+        ${args} \\
+        -x \$db_name \\
+        ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -32,7 +35,7 @@ process CENTRIFUGE_KREPORT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt

diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
@@ -29,7 +29,7 @@ profiles {
         docker.enabled          = true
         docker.userEmulation    = false
         docker.fixOwnership     = true
-        docker.runOptions       = '--platform=linux/amd64 --security-opt=no-new-privileges'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'