adopt spades v4

BCCDC-PHL · Jul 10, 2024 · 4897e7e · 4897e7e
1 parent 455ae76
commit 4897e7e
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/environment.yaml b/environment.yaml
@@ -9,7 +9,7 @@ dependencies:
   - blast=2.14.1
   - bwa=0.7.17
   - samtools=1.17
-  - spades=3.15.3
+  - spades=4.0.0
   - clustalw=2.1
   - freebayes=1.3.6
   - python=3

diff --git a/fluviewer/analysis.py b/fluviewer/analysis.py
@@ -235,7 +235,7 @@ def assemble_contigs(
 
     os.makedirs(spades_output, exist_ok=True)
 
-    terminal_command = (f'spades.py --rnaviral --isolate -1 {fwd_reads} '
+    terminal_command = (f'spades.py --rnaviral -1 {fwd_reads} '
                         f'-2 {rev_reads} -o {spades_output}')
 
     process_name = 'spades'