Merge pull request #103 from genomic-medicine-sweden/update_filtlong

Update the dev branch with the filtlong update

modules.json

@@ -37,7 +37,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "filtlong": {
-                "git_sha": "089f761f0bf79c4a486f1df9b6205f650196a2c1"
+                "git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
             },
             "gunzip": {
                 "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"

modules/nf-core/modules/filtlong/main.nf

@@ -12,7 +12,8 @@ process FILTLONG {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
-    path "versions.yml"                                     , emit: versions
+    tuple val(meta), path("*.log")     , emit: log
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,6 +28,7 @@ process FILTLONG {
         $short_reads \\
         $args \\
         $longreads \\
+        2> ${prefix}.log \\
         | gzip -n > ${prefix}.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/modules/filtlong/meta.yml

@@ -45,6 +45,11 @@ output:
       type: file
       description: Filtered (compressed) fastq file
       pattern: "*.fastq.gz"
+  - log:
+      type: file
+      description: Standard error logging file containing summary statistics
+      pattern: "*.log"
 
 authors:
   - "@d4straub"
+  - "@sofstam"

subworkflows/local/longread_preprocessing.nf

@@ -30,6 +30,7 @@ workflow LONGREAD_PREPROCESSING {
 
         ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
         ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
 
     } else {
         PORECHOP ( reads )
@@ -45,6 +46,7 @@ workflow LONGREAD_PREPROCESSING {
 
         ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
         ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
 
     }