removing bash setting typo

Author: nrminor

modules/seqkit.nf

@@ -16,7 +16,7 @@ process SORT_AND_COMPRESS_TO_FASTA {
     script:
 	barcode = file(reads).getSimpleName()
     """
-    set -eou pipefile
+    set -eou pipefail
 
     mkdir -p tmp
 

nextflow.config

@@ -139,18 +139,18 @@ params {
     // nextclade dataset
     nextclade_dataset = null
 
-	// Dataset, either a local FASTA file or a pre-built dataset built by Sylph, to use
-	// for metagenomic profiling
-	meta_ref = null
+		// Dataset, either a local FASTA file or a pre-built dataset built by Sylph, to use
+		// for metagenomic profiling
+		meta_ref = null
 
-	// Contamination FASTA dataset to scrub from reads
-	contam_fasta = null
+		// Contamination FASTA dataset to scrub from reads
+		contam_fasta = null
 
-	// K-mer size to use for metagenomic sketching
-	k = 31
+		// K-mer size to use for metagenomic sketching
+		k = 31
 
-	// devider haplotype phasing preset
-	devider_preset = "nanopore-r10" // old-long-reads, nanopore-r9, nanopore-r10, hi-fi
+		// devider haplotype phasing preset
+		devider_preset = "nanopore-r10" // old-long-reads, nanopore-r9, nanopore-r10, hi-fi
 
     // nextclade dataset cache
     nextclade_cache = "$launchDir/work/nextclade_datasets"
@@ -161,6 +161,10 @@ params {
     // Where to place results
     results = "$launchDir/results"
 
+		// Whether to run in low-memory mode, which limits the number of parallel instances
+		// of high-memory files
+		low_memory = null
+
     // whether to cleanup work directory after a successful run (defaults to false)
     cleanup = null