allow mashtree to download assemblies

bactopia · Jun 2, 2023 · 69d251c · 69d251c
1 parent f7611ad
commit 69d251c
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/conf/workflows.config b/conf/workflows.config
@@ -5,14 +5,14 @@ params {
         bactopia = ['bactopia', 'staphopia', 'cleanyerreads', 'teton', 'updater']
         'bactopiatools' {
             subworkflows = [
-                'ariba', 'bakta', 'eggnog', 'gtdb', 'merlin', 'pangenome', 'scrubber', 'snippy',
-                'staphtyper'
+                'ariba', 'bakta', 'eggnog', 'gtdb', 'mashtree', 'merlin', 'pangenome',
+                'scrubber', 'snippy', 'staphtyper'
             ]
             modules = [
                 'abricate', 'agrvate', 'amrfinderplus', 'blastn', 'blastp', 'blastx', 'busco',
                 'bracken', 'checkm', 'ectyper', 'emmtyper', 'fastani', 'gamma', 'genotyphi',
                 'hicap', 'hpsuissero', 'ismapper', 'kleborate', 'kraken2', 'legsta', 'lissero',
-                'mashdist', 'mashtree', 'mcroni', 'meningotype', 'midas', 'mlst', 'mobsuite',
+                'mashdist', 'mcroni', 'meningotype', 'midas', 'mlst', 'mobsuite',
                 'mykrobe', 'ngmaster', 'pasty', 'pbptyper', 'plasmidfinder', 'quast', 'rgi',
                 'seqsero2', 'seroba', 'shigatyper', 'shigeifinder', 'sistr', 'spatyper',
                 'ssuissero', 'staphopiasccmec', 'stecfinder', 'tblastn', 'tblastx', 'tbprofiler',
@@ -102,6 +102,12 @@ params {
             ext = "fna"
             modules = ["gtdbtk_setupdb", "gtdbtk_classifywf"]
         }
+        'mashtree' {
+            description = "Create a trees using Mash distances"
+            ext = "fna"
+            path = "modules/nf-core/mashtree"
+            modules = ["ncbigenomedownload"]
+        }
         'merlin' {
             description = "MinmER assisted species-specific bactopia tool seLectIoN"
             ext = "fna_fastq"
@@ -297,11 +303,6 @@ params {
             ext = "fna"
             path = "modules/nf-core/mash/dist"
         }
-        'mashtree' {
-            description = "Create a trees using Mash distance"
-            ext = "fna"
-            path = "modules/nf-core/mashtree"
-        }
         'mcroni' {
             description = "Sequence variation in mobilized colistin resistance (mcr-1) genes"
             ext = "fna"

diff --git a/subworkflows/local/fastani/main.nf b/subworkflows/local/fastani/main.nf
@@ -17,7 +17,6 @@ include { CSVTK_CONCAT } from '../../../modules/nf-core/csvtk/concat/main' addPa
 workflow FASTANI {
     take:
     query // channel: [ val(meta), [ fasta ] ]
-    reference // channel: [ fastas ]
 
     main:
     ch_versions = Channel.empty()