Merge remote-tracking branch 'origin/dev' into porechop-log

conf/modules.config

@@ -145,7 +145,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/filtlong" },
             mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz',
+            pattern: '*.{fastq.gz,log}',
             enabled: params.save_preprocessed_reads
         ]
     }
@@ -347,6 +347,7 @@ process {
     }
 
     withName: CENTRIFUGE_KREPORT {
+        errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
@@ -386,7 +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

@@ -22,13 +22,13 @@
                 "git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
             },
             "centrifuge/kreport": {
-                "git_sha": "be4ae28c3c95b3c4047a7d9fb4cb0ed749631cea"
+                "git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
             },
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "diamond/blastx": {
-                "git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
+                "git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
             },
             "fastp": {
                 "git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"

modules/nf-core/modules/centrifuge/kreport/main.nf

@@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT {
         'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
 
     input:
-    tuple val(meta), path(results)
+    tuple val(meta), path(report)
     path db
 
     output:
@@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/.1.cf//'`
-    centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
+    centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/modules/centrifuge/kreport/meta.yml

@@ -15,9 +15,9 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - results:
+  - report:
       type: file
-      description: File containing the centrifuge classification results
+      description: File containing the centrifuge classification report
       pattern: "*.{txt}"
 
 output:

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

@@ -148,7 +148,7 @@ workflow PROFILING {
                                 }
 
         CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads  )
-        CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
+        CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.report, ch_input_for_centrifuge.db)
         ch_versions            = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
         ch_raw_profiles        = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
@@ -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 ) 
 
     }