From ca8e5ae948ac6a31cc077d50d1c0d9ddf29be5dc Mon Sep 17 00:00:00 2001
From: lvreynoso <lreynoso@chanzuckerberg.com>
Date: Mon, 22 Apr 2024 11:51:52 -0700
Subject: [PATCH] Use shlex.split() on diamond_args; use --sensitive diamond
 option

---
 lib/idseq_utils/idseq_utils/diamond_scatter.py   | 5 ++++-
 scripts/release.sh                               | 4 ++++
 workflows/long-read-mngs/run.wdl                 | 4 ++--
 workflows/short-read-mngs/non_host_alignment.wdl | 2 +-
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/lib/idseq_utils/idseq_utils/diamond_scatter.py b/lib/idseq_utils/idseq_utils/diamond_scatter.py
index 385301c1d..e1710171c 100644
--- a/lib/idseq_utils/idseq_utils/diamond_scatter.py
+++ b/lib/idseq_utils/idseq_utils/diamond_scatter.py
@@ -3,6 +3,7 @@
 """
 
 import os
+import shlex
 import shutil
 import sys
 import errno
@@ -71,8 +72,10 @@ def diamond_blastx(
         database,
         "--out",
         out,
-        f"--{diamond_args}",
     ]
+
+    cmd.extend(shlex.split(diamond_args))
+
     for query in queries:
         cmd += ["--query", query]
     if chunk:
diff --git a/scripts/release.sh b/scripts/release.sh
index da13b1e74..ec0dc9884 100755
--- a/scripts/release.sh
+++ b/scripts/release.sh
@@ -28,6 +28,10 @@ else
     exit 1
 fi
 
+if [[ $WORKFLOW_NAME == long-read-mngs ]]; then
+    TAG="long-read-mngs-v0.7.6-branch-diamondsensitive"
+fi
+
 if [[ $( git branch --show-current) != "main" ]]; then 
     COMMIT=$(git rev-parse --short HEAD)
     TAG=$TAG"-$COMMIT"
diff --git a/workflows/long-read-mngs/run.wdl b/workflows/long-read-mngs/run.wdl
index 820a5c85a..8c4794f59 100644
--- a/workflows/long-read-mngs/run.wdl
+++ b/workflows/long-read-mngs/run.wdl
@@ -612,7 +612,7 @@ task RunNRAlignment {
 
         if [[ "~{run_locally}" == true ]]; then
           diamond makedb --in "~{local_diamond_index}" -d reference
-          diamond blastx -d reference -q "~{assembled_reads_fa}" -o "diamond.m8" "--~{diamond_args}"
+          diamond blastx -d reference -q "~{assembled_reads_fa}" -o "diamond.m8" "~{diamond_args}"
         else
           python3 <<CODE
         import os
@@ -1297,7 +1297,7 @@ workflow czid_long_read_mngs {
         String minimap2_prefix = "gsnap"
 
         String? diamond_db
-        String diamond_args = "long-reads"
+        String diamond_args = "--long-reads --sensitive"
 
         Boolean use_deuterostome_filter = true
         Boolean use_taxon_whitelist = false
diff --git a/workflows/short-read-mngs/non_host_alignment.wdl b/workflows/short-read-mngs/non_host_alignment.wdl
index 9f60b721e..e1da22034 100644
--- a/workflows/short-read-mngs/non_host_alignment.wdl
+++ b/workflows/short-read-mngs/non_host_alignment.wdl
@@ -299,7 +299,7 @@ workflow czid_non_host_alignment {
     String minimap2_db = "s3://czid-public-references/minimap2-test/2021-01-22/nt_k14_w8_20/"
     String diamond_db = "s3://czid-public-references/diamond-test/2021-01-22/"
     String minimap2_args = "-cx sr --secondary=yes"
-    String diamond_args = "mid-sensitive"
+    String diamond_args = "--mid-sensitive"
     String minimap2_prefix = "gsnap"
     String diamond_prefix = "rapsearch2"