Merge pull request #190 from danilodileo/eukulele-download

Eukulele download module removed
nf-core · Oct 6, 2023 · 11ec34c · 11ec34c
2 parents 815c763 + 0bcdbbe
commit 11ec34c
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Showing 5 changed files with 6 additions and 65 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -348,15 +348,6 @@ process {
         ]
     }
 
-    withName: EUKULELE_DOWNLOAD {
-        ext.when = { db }
-        publishDir = [
-            path: { "${params.eukulele_dbpath}/" },
-            mode: 'copy',
-            pattern: "*"
-        ]
-    }
-
     withName: EUKULELE_SEARCH {
         publishDir = [
             path: { "${params.outdir}/eukulele" },

diff --git a/modules/local/eukulele/download.nf b/modules/local/eukulele/download.nf
diff --git a/modules/local/eukulele/search.nf b/modules/local/eukulele/search.nf
@@ -2,10 +2,10 @@ process EUKULELE_SEARCH {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::eukulele=2.0.3"
+    conda "bioconda::eukulele=2.0.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/eukulele:2.0.3--pyh723bec7_0' :
-        'biocontainers/eukulele:2.0.3--pyh723bec7_0' }"
+        'https://depot.galaxyproject.org/singularity/eukulele:2.0.5--pyh723bec7_0' :
+        'biocontainers/eukulele:2.0.5--pyh723bec7_0' }"
 
     input:
     tuple val(meta), path(fasta), val(dbname), path(eukdb)

diff --git a/subworkflows/local/eukulele.nf b/subworkflows/local/eukulele.nf
@@ -3,7 +3,6 @@
 //
 
 include { EUKULELE_SEARCH                   } from '../../modules/local/eukulele/search'
-include { EUKULELE_DOWNLOAD                 } from '../../modules/local/eukulele/download'
 include { FORMAT_TAX                        } from '../../modules/local/format_tax'
 include { SUM_TAXONOMY                      } from '../../modules/local/sum_taxonomy'
 
@@ -16,22 +15,12 @@ workflow SUB_EUKULELE {
     main:
         ch_versions = Channel.empty()
 
-
-        EUKULELE_DOWNLOAD ( eukulele.filter { it[2] }.map { [ it[2], it[3] ] } )
-        ch_download = EUKULELE_DOWNLOAD.out.db
-
-        Channel.empty()
-            .mix ( EUKULELE_DOWNLOAD.out.db )
-            .mix(eukulele.filter{ ! it[2] }.map { [ [], it[3] ] } )
-            .merge( eukulele.map{ [ it[0], it[1] ] } )
-            .map { [ [ id: "${it[2].id}.${it[0]}" ], it[3], it[0], it[1] ] } 
-            .set { ch_eukulele }
-        EUKULELE_SEARCH( ch_eukulele )
+        EUKULELE_SEARCH( eukulele )
 
         FORMAT_TAX( EUKULELE_SEARCH.out.taxonomy_estimation.map { [ it[0], it[1] ] } )
 
         FORMAT_TAX.out.tax
-            .join(ch_eukulele)
+            .join(eukulele)
             .map { [ it[0], it[3], it[1] ] }
             .set { ch_sum_taxonomy }
 

diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf
@@ -524,6 +524,7 @@ workflow METATDENOVO {
                 .set { ch_eukulele }
             SUB_EUKULELE( ch_eukulele, ch_fcs_for_summary )
             ch_taxonomy_summary = SUB_EUKULELE.out.taxonomy_summary.collect().map { it[1] }
+            ch_versions = ch_versions.mix(SUB_EUKULELE.out.versions)
             ch_merge_tables
                 .combine( ch_taxonomy_summary )
                 .set { ch_merge_tables }