refactor: Gzip DIAMOND outs

dalmolingroup · Sep 28, 2023 · 0613ab9 · 0613ab9
1 parent 361c766
commit 0613ab9
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/bin/annotate.py b/bin/annotate.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+import gzip
 import plyvel
 import os
 import time
@@ -42,7 +43,7 @@ def getAll(
 ):
     check = True
     query = None
-    with open(input, "r") as f:
+    with gzip.open(input, "rb") as f:
         write(out, "Query", "Annotation")
         for line in f:
             ls = line.split(sep)
@@ -105,7 +106,7 @@ def getBestHits(
     match = False
     check = True
     query = None
-    with open(input, "r") as f:
+    with gzip.open(input, "rb") as f:
         write(out, "Query", "Annotation")
         for line in f:
             ls = line.split(sep)

diff --git a/conf/modules.config b/conf/modules.config
@@ -78,7 +78,7 @@ process {
 
     // Alignment
     withName: DIAMOND_BLASTX {
-        ext.args = '--more-sensitive --top 3'
+        ext.args = '--more-sensitive --top 3 --compress 1'
         publishDir = [
             path: { "${params.outdir}/alignment/${meta.id}" },
             mode: params.publish_dir_mode,