From 1869c2feac02aeea374852c421df793fd69e290c Mon Sep 17 00:00:00 2001
From: Biowilko <sam1.wilkinson1@gmail.com>
Date: Wed, 21 Jun 2023 13:22:26 +0100
Subject: [PATCH 1/3] Up resources available to bgzip taxon fastqs

---
 modules/extract_taxa.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/extract_taxa.nf b/modules/extract_taxa.nf
index 337b541..e3e8198 100644
--- 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'
 
@@ -56,7 +56,7 @@ process extract_reads {
 
     conda 'bioconda::biopython=1.78 bioconda::tabix=1.11'
     container "biowilko/scylla@${params.wf.container_sha}"   
-    
+
     input:
         val unique_id
         path fastq

From 3e017d2fbf064f9a74b98193b079785d04022e5d Mon Sep 17 00:00:00 2001
From: Biowilko <sam1.wilkinson1@gmail.com>
Date: Wed, 21 Jun 2023 13:28:19 +0100
Subject: [PATCH 2/3] Re-enable human threshold fail

---
 bin/extract_kraken_reads.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/extract_kraken_reads.py b/bin/extract_kraken_reads.py
index 7abbac6..c8e4b10 100755
--- 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] = {
@@ -533,7 +533,7 @@ 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,

From 6ac4a84f9c567b020ba25ca32e3863f3739939f1 Mon Sep 17 00:00:00 2001
From: Biowilko <sam1.wilkinson1@gmail.com>
Date: Wed, 21 Jun 2023 13:52:10 +0100
Subject: [PATCH 3/3] increase extract_reads resource again

---
 modules/extract_taxa.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/extract_taxa.nf b/modules/extract_taxa.nf
index e3e8198..dd6b434 100644
--- a/modules/extract_taxa.nf
+++ b/modules/extract_taxa.nf
@@ -50,7 +50,7 @@ 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'