fixing nanopore freyja error

BU-ISCIII · Aug 16, 2023 · 8c74f8f · 8c74f8f
1 parent a768d54
commit 8c74f8f
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/conf/modules_illumina.config b/conf/modules_illumina.config
@@ -208,7 +208,7 @@ if (!params.skip_variants) {
                 ]
             }
             withName: 'FREYJA_BOOT' {
-                ext.args = '--boxplot PDF'
+                ext.args = '--boxplot pdf'
                 publishDir = [
                     path: { "${params.outdir}/variants/freyja/bootstrap" },
                     mode: params.publish_dir_mode,

diff --git a/conf/modules_nanopore.config b/conf/modules_nanopore.config
@@ -248,7 +248,7 @@ if (!params.skip_freyja) {
         }
 
         withName: 'FREYJA_BOOT' {
-            ext.args = '--boxplot PDF'
+            ext.args = '--boxplot pdf'
             publishDir = [
                 path: { "${params.outdir}/${params.artic_minion_caller}/freyja/bootstrap" },
                 mode: params.publish_dir_mode,

diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf
@@ -432,7 +432,7 @@ workflow NANOPORE {
     if (!params.skip_freyja) {
         BAM_VARIANT_DEMIX_BOOT_FREYJA(
             ARTIC_MINION.out.bam_primertrimmed,
-            ARTIC_MINION.out.fasta,
+            PREPARE_GENOME.out.fasta,
             params.freyja_repeats,
             params.freyja_db_name,
             params.freyja_barcodes,