Merge branch 'main' of https://github.com/BioWilko/scylla into main

artic-network · Jun 21, 2023 · 9ff72e7 · 9ff72e7
2 parents 194a852 + 6ac4a84
commit 9ff72e7
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/bin/extract_kraken_reads.py b/bin/extract_kraken_reads.py
@@ -76,7 +76,7 @@ def get_bracken_hierarchy(kraken_file, bracken_file, max_human=None):
                         "ERROR: found %i human reads, max allowed is %i\n"
                         % (num_direct, max_human)
                     )
-                    # sys.exit(2)
+                    sys.exit(2)
                 continue
 
             entries[ncbi] = {
@@ -534,7 +534,7 @@ def main():
         args.reads2,
         args.prefix,
         max_human=args.max_human,
-        names = args.taxid,
+        names=args.taxid,
         target_ranks=target_ranks,
         min_count=args.min_count,
         min_count_descendants=args.min_count_descendants,

diff --git a/modules/extract_taxa.nf b/modules/extract_taxa.nf
@@ -9,7 +9,7 @@
 // in config so could be good dehuman sanity check
 process extract_paired_reads {
 
-    label 'process_medium'
+    label 'process_high'
 
     publishDir path: "${params.out_dir}/${unique_id}/reads_by_taxa", mode: 'copy'
 
@@ -50,13 +50,13 @@ process extract_paired_reads {
 
 process extract_reads {
 
-    label 'process_medium'
+    label 'process_high'
 
     publishDir path: "${params.out_dir}/${unique_id}/reads_by_taxa", mode: 'copy'
 
     conda 'bioconda::biopython=1.78 bioconda::tabix=1.11'
     container "biowilko/scylla@${params.wf.container_sha}"   
-    
+
     input:
         val unique_id
         path fastq