Fix kraken2 module

2024-11-24 16:59:55 +00:00 · 2022-03-28 16:46:45 +02:00 · 2022-03-28 16:46:45 +02:00 · 98dc8014a5
commit 98dc8014a5
parent 231253227c
2 changed files with 5 additions and 6 deletions
--- a/modules.json
+++ b/modules.json
@ -24,11 +24,11 @@
            "multiqc": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
-            "untar": {
-                "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
-            },
            "porechop": {
                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+            },
+            "untar": {
+                "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
            }
        }
    }
--- a/modules/nf-core/modules/kraken2/kraken2/main.nf
+++ b/modules/nf-core/modules/kraken2/kraken2/main.nf
@ -32,13 +32,12 @@ process KRAKEN2_KRAKEN2 {
        --threads $task.cpus \\
        --unclassified-out $unclassified \\
        --classified-out $classified \\
-        $args \\
        --report ${prefix}.kraken2.report.txt \\
        --gzip-compressed \\
        $paired \\
+        $args \\
        $reads

-
    pigz -p $task.cpus *.fastq

    cat <<-END_VERSIONS > versions.yml