Fix MALT multiqc report clash

modules.json

@@ -19,7 +19,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "malt/run": {
-                "git_sha": "76cdd46f3f8a77fb5023fb5a39c4ab99925b8b56"
+                "git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
             },
             "multiqc": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"

modules/nf-core/modules/malt/run/main.nf

@@ -23,6 +23,7 @@ process MALT_RUN {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def avail_mem = 6
     if (!task.memory) {
         log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
@@ -39,7 +40,7 @@ process MALT_RUN {
         $args \\
         --inFile ${fastqs.join(' ')} \\
         -m $mode \\
-        --index $index/ |&tee malt-run.log
+        --index $index/ |&tee ${prefix}-malt-run.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/modules/malt/run/meta.yml

@@ -52,7 +52,7 @@ output:
   - log:
       type: file
       description: Log of verbose MALT stdout
-      pattern: "malt-run.log"
+      pattern: "*-malt-run.log"
 
 authors:
   - "@jfy133"

workflows/taxprofiler.nf

@@ -203,7 +203,8 @@ workflow TAXPROFILER {
         ch_versions = ch_versions.mix(MALT_RUN.out.versions.first())
     }
 
-
+    // TODO MALT results overwriting per database?
+    // TODO Versions for Karken/MALT not report?
     MULTIQC (
         ch_multiqc_files.collect()
     )