Update DIAMOND module to output log file (#1879)

* Update DIAMOND module to output log file

* Updating DIAMOND module to output log file - with jfy133 suggestions

Co-authored-by: Mahwash Jamy <mahwashjamy@n183-p186.eduroam.kth.se>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

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/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"

tests/modules/diamond/blastx/test.yml

@@ -1,18 +1,21 @@
 - name: diamond blastx test_diamond_blastx
-  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config  -c ./tests/modules/diamond/blastx/nextflow.config
   tags:
     - diamond
     - diamond/blastx
   files:
+    - path: output/diamond/proteome.fasta.dmnd
+    - path: output/diamond/test.diamond_blastx.log
+      contains: ["queries aligned"]
     - path: output/diamond/test.diamond_blastx.txt
-    - path: output/diamond/versions.yml
 
 - name: diamond blastx test_diamond_blastx_daa
-  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c ./tests/config/nextflow.config  -c ./tests/modules/diamond/blastx/nextflow.config
   tags:
     - diamond
     - diamond/blastx
   files:
+    - path: output/diamond/proteome.fasta.dmnd
     - path: output/diamond/test.diamond_blastx.daa
-      md5sum: 0df4a833408416f32981415873facc11
-    - path: output/diamond/versions.yml
+    - path: output/diamond/test.diamond_blastx.log
+      contains: ["queries aligned"]