Merge branch 'dev' into update_filtlong

conf/modules.config

@@ -391,6 +391,7 @@ process {
     }
 
     withName: MOTUS_PROFILE {
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/motus/${meta.db_name}" },
             mode: params.publish_dir_mode

modules.json

@@ -79,7 +79,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "motus/profile": {
-                "git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
+                "git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
             },
             "multiqc": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

modules/nf-core/modules/motus/profile/main.nf

@@ -15,6 +15,7 @@ process MOTUS_PROFILE {
     tuple val(meta), path("*.out"), emit: out
     tuple val(meta), path("*.bam"), optional: true, emit: bam
     tuple val(meta), path("*.mgc"), optional: true, emit: mgc
+    tuple val(meta), path("*.log")                , emit: log
     path "versions.yml"           , emit: versions
 
     when:
@@ -36,7 +37,8 @@ process MOTUS_PROFILE {
         $refdb \\
         -t $task.cpus \\
         -n $prefix \\
-        -o ${prefix}.out
+        -o ${prefix}.out \\
+        2> ${prefix}.log
 
     ## mOTUs version number is not available from command line.
     ## mOTUs save the version number in index database folder.
@@ -48,7 +50,7 @@ process MOTUS_PROFILE {
     fi
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        mOTUs: \$VERSION
+        motus: \$VERSION
     END_VERSIONS
     """
 }

modules/nf-core/modules/motus/profile/meta.yml

@@ -56,6 +56,10 @@ output:
       type: file
       description: Optional intermediate mgc read count table file saved with `-M`.
       pattern: "*.{mgc}"
+  - log:
+      type: file
+      description: Standard error logging file containing summary statistics
+      pattern: "*.log"
 
 authors:
   - "@jianhong"

subworkflows/local/profiling.nf

@@ -227,6 +227,7 @@ workflow PROFILING {
         MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
         ch_versions        = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
+        ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
 
     }