Fix: arriba: rename argument and reorder alphabetically

modules/nf-core/arriba/arriba/main.nf

@@ -4,16 +4,17 @@ process ARRIBA_ARRIBA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/arriba:2.4.0--h0033a41_2' :
-        'biocontainers/arriba:2.4.0--h0033a41_2' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbbd3ccedb1663939f2ca075a071e75b0d1c60f19a4cd46dd9ffe371f133105a/data' :
+        'community.wave.seqera.io/library/arriba:2.4.0--9680480f3735ac7f' }"
+
 
     input:
     tuple val(meta),  path(bam)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(gtf)
     path(blacklist)
-    path(known_fusions)
     path(cytobands)
+    path(known_fusions)
     path(protein_domains)
 
     output:
@@ -27,10 +28,10 @@ process ARRIBA_ARRIBA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
-    def known_fusions = known_fusions ? "-k $known_fusions" : ""
-    def cytobands = cytobands ? "-d $cytobands" : ""
-    def protein_domains = protein_domains ? "-p $protein_domains" : ""
+    def arg_blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
+    def arg_cytobands = cytobands ? "-d $cytobands" : ""
+    def arg_known_fusions = known_fusions ? "-k $known_fusions" : ""
+    def arg_protein_domains = protein_domains ? "-p $protein_domains" : ""
 
     """
     arriba \\
@@ -39,10 +40,10 @@ process ARRIBA_ARRIBA {
         -g $gtf \\
         -o ${prefix}.fusions.tsv \\
         -O ${prefix}.fusions.discarded.tsv \\
-        $blacklist \\
-        $known_fusions \\
-        $cytobands \\
-        $protein_domains \\
+        $arg_blacklist \\
+        $arg_cytobands \\
+        $arg_known_fusions \\
+        $arg_protein_domains \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/arriba/arriba/meta.yml

@@ -47,14 +47,14 @@ input:
         type: file
         description: Blacklist file
         pattern: "*.{tsv}"
-  - - known_fusions:
-        type: file
-        description: Known fusions file
-        pattern: "*.{tsv}"
   - - cytobands:
         type: file
         description: Cytobands file
         pattern: "*.{tsv}"
+  - - known_fusions:
+        type: file
+        description: Known fusions file
+        pattern: "*.{tsv}"
   - - protein_domains:
         type: file
         description: Protein domains file

modules/nf-core/arriba/arriba/tests/nextflow.config

@@ -1,3 +1,8 @@
+profiles {
+    docker {
+        docker.runOptions = '-u $(id -u):$(id -g)'
+    }
+}
 process {
     withName: STAR_GENOMEGENERATE {
         ext.args = '--genomeSAindexNbases 11'

modules/nf-core/arriba/download/environment.yml

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::arriba=2.4.0
+  - conda-forge::wget=1.21.4

modules/nf-core/arriba/download/main.nf

@@ -4,9 +4,8 @@ process ARRIBA_DOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/arriba:2.4.0--h0033a41_2' :
-        'biocontainers/arriba:2.4.0--h0033a41_2' }"
-
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3b/3b54fa9135194c72a18d00db6b399c03248103f87e43ca75e4b50d61179994b3/data' :
+        'community.wave.seqera.io/library/wget:1.21.4--8b0fcde81c17be5e' }"
     input:
     val(genome)
 
@@ -30,20 +29,20 @@ process ARRIBA_DOWNLOAD {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        arriba_download: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
+        wget: \$(wget --version | head -1 | sed 's/GNU Wget //' | sed -E 's/(.*) built on darwin.*/\1/')
     END_VERSIONS
     """
 
     stub:
     """
     touch blacklist_hg38_GRCh38_v2.4.0.tsv.gz
-    touch protein_domains_hg38_GRCh38_v2.4.0.gff3
     touch cytobands_hg38_GRCh38_v2.4.0.tsv
+    touch protein_domains_hg38_GRCh38_v2.4.0.gff3
     touch known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        arriba_download: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
+        wget: \$(wget --version | head -1 | sed 's/GNU Wget //' | sed -E 's/(.*) built on darwin.*/\1/')
     END_VERSIONS
     """
 }

modules/nf-core/arriba/download/tests/main.nf.test

@@ -11,6 +11,7 @@ nextflow_process {
     tag "arriba/download"
 
     test("test-arriba-download") {
+        config "./nextflow.config"
         when {
             process {
                 """
@@ -29,6 +30,7 @@ nextflow_process {
     }
 
     test("download - stub") {
+        config "./nextflow.config"
 
         options "-stub"
 

modules/nf-core/arriba/download/tests/main.nf.test.snap

@@ -15,7 +15,7 @@
                     "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz:md5,4f00f81ccb5f4db283f1a22b8b0da67c"
                 ],
                 "4": [
-                    "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893"
+                    "versions.yml:md5,e94a685b433b6749e129af0f799f614c"
                 ],
                 "blacklist": [
                     "blacklist_hg38_GRCh38_v2.4.0.tsv.gz:md5,e3098a4be51aece78aede64b55c39318"
@@ -30,14 +30,14 @@
                     "protein_domains_hg38_GRCh38_v2.4.0.gff3:md5,43c387a784ebeed71b4147076cebf978"
                 ],
                 "versions": [
-                    "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893"
+                    "versions.yml:md5,e94a685b433b6749e129af0f799f614c"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-16T01:46:32.110653034"
+        "timestamp": "2025-01-14T14:01:45.101697"
     }
 }

modules/nf-core/arriba/download/tests/nextflow.config

@@ -0,0 +1,5 @@
+profiles {
+    docker {
+        docker.runOptions = '-u $(id -u):$(id -g)'
+    }
+}