Merge pull request #105 from genomic-medicine-sweden/diamond-update

Update the dev branch with the DIAMOND module update

conf/modules.config

@@ -387,7 +387,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/diamond/${meta.db_name}" },
             mode: params.publish_dir_mode,
-            pattern: '*.{blast,xml,txt,daa,sam,tsv,paf}'
+            pattern: '*.{blast,xml,txt,daa,sam,tsv,paf,log}'
         ]
     }
 

modules.json

@@ -28,7 +28,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "diamond/blastx": {
-                "git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
+                "git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
             },
             "fastp": {
                 "git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"

modules/nf-core/modules/diamond/blastx/main.nf

@@ -21,6 +21,7 @@ process DIAMOND_BLASTX {
     tuple val(meta), path('*.sam')  , optional: true, emit: sam
     tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
     tuple val(meta), path('*.paf')  , optional: true, emit: paf
+    tuple val(meta), path("*.log")                  , emit: log
     path "versions.yml"                               , emit: versions
 
     when:
@@ -54,7 +55,10 @@ process DIAMOND_BLASTX {
         --query $fasta \\
         --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${out_ext}
+        --out ${prefix}.${out_ext} \\
+        --log
+
+    mv diamond.log ${prefix}.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/modules/diamond/blastx/meta.yml

@@ -70,7 +70,12 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - log:
+      type: file
+      description: Log file containing stdout information
+      pattern: "*.{log}"
 
 authors:
   - "@spficklin"
   - "@jfy133"
+  - "@mjamy"

subworkflows/local/profiling.nf

@@ -208,6 +208,7 @@ workflow PROFILING {
         DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format , [] )
         ch_versions        = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )
+        ch_multiqc_files   = ch_multiqc_files.mix( DIAMOND_BLASTX.out.log ) 
 
     }