Merge pull request #304 from erikrikarddaniel/fix-eukulele-gzip

Make eukulele count files optional

CHANGELOG.md

@@ -24,6 +24,7 @@ Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co
 
 ### `Fixed`
 
+- [#304](<[https://github.com/nf-core/ampliseq/pull/681](https://github.com/nf-core/metatdenovo/pull/304)>) - Make EUKulele counts output optional as it's not always created
 - [#269](<[https://github.com/nf-core/ampliseq/pull/681](https://github.com/nf-core/metatdenovo/pull/269)>) - Make Transdecoder work better with `-resume`
 
 ### `Dependencies`

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/metatdenovo/master/assets/schema_input.json",
     "title": "nf-core/metatdenovo pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",

modules/local/eukulele/search.nf

@@ -12,7 +12,7 @@ process EUKULELE_SEARCH {
 
     output:
     tuple val(meta), path("*/taxonomy_estimation/*.out.gz"), val("${dbname}") , emit: taxonomy_estimation
-    tuple val(meta), path("*/taxonomy_counts/*.csv.gz")                       , emit: taxonomy_counts
+    tuple val(meta), path("*/taxonomy_counts/*.csv.gz")                       , emit: taxonomy_counts    , optional: true
     tuple val(meta), path("*/mets_full/diamond/*")                            , emit: diamond
 
     path "versions.yml"                                                       , emit: versions
@@ -38,7 +38,7 @@ process EUKULELE_SEARCH {
         contigs || rc=\$?
 
     gzip ${prefix}/mets_full/diamond/*.out
-    gzip ${prefix}/taxonomy_counts/*.csv
+    find ${prefix}/taxonomy_counts/ -name "*.csv" | xargs gzip
     gzip ${prefix}/taxonomy_estimation/*.out
 
     cat <<-END_VERSIONS > versions.yml

nextflow_schema.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/metatdenovo/master/nextflow_schema.json",
     "title": "nf-core/metatdenovo pipeline parameters",
     "description": "Assembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic",