update trinity params

Joon-Klaps · Jul 9, 2024 · 644676c · 644676c
1 parent aa76a75
commit 644676c
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -404,7 +404,7 @@ process {
 
         withName: TRINITY {
             ext.prefix    = { "${meta.id}_trinity" }
-            ext.args      = "--NO_SEQTK"
+            ext.args      = "--max_reads_per_graph 100000"  // subsample to 100k reads - mimic viral ngs
             publishDir = [
                 path: { "${params.outdir}/assembly/assemblers/trinity/contigs" },
                 mode: params.publish_dir_mode,
@@ -1160,7 +1160,7 @@ process {
                     "${params.outdir}/variants/bcftools/${meta.sample}" :
                     "${params.outdir}/assembly/polishing/iterations/${meta.step}/variants/bcftools" },
                 mode: params.publish_dir_mode,
-                pattern: '*.mpileup.gz',
+                pattern: '*.{bcf,vcf,bcf.gz,vcf.gz,.mpileup.gz}',
                 saveAs: { filename -> params.prefix || params.global_prefix  ? "${params.global_prefix}-$filename" : filename }
             ]
         }