From 2a8c304f610ca70ca7b644acf5d7c519cad4c2f1 Mon Sep 17 00:00:00 2001
From: Andrew Hale <107064135+awh082834@users.noreply.github.com>
Date: Thu, 16 Jan 2025 15:46:17 -0500
Subject: [PATCH] [srst2_vibrio, merlin_magic] Removed instances of srst2_ from
 inputs (#726)

* Removed instances of srst2_ from inputs

* Update md5sum of wf_merlin_magic for wf_theiaprok_illumina_pe and se
---
 .../vibrio/task_srst2_vibrio.wdl              | 20 +++++++++----------
 .../test_wf_theiaprok_illumina_pe.yml         |  2 +-
 .../test_wf_theiaprok_illumina_se.yml         |  2 +-
 workflows/utilities/wf_merlin_magic.wdl       | 10 +++++-----
 4 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/tasks/species_typing/vibrio/task_srst2_vibrio.wdl b/tasks/species_typing/vibrio/task_srst2_vibrio.wdl
index 55ea52235..5af3ae2d9 100644
--- a/tasks/species_typing/vibrio/task_srst2_vibrio.wdl
+++ b/tasks/species_typing/vibrio/task_srst2_vibrio.wdl
@@ -8,11 +8,11 @@ task srst2_vibrio {
     File read1
     File? read2
     String samplename
-    Int srst2_min_cov
-    Int srst2_max_divergence
-    Int srst2_min_depth
-    Int srst2_min_edge_depth
-    Int srst2_gene_max_mismatch
+    Int min_cov
+    Int max_divergence
+    Int min_depth
+    Int min_edge_depth
+    Int gene_max_mismatch
     String docker = "us-docker.pkg.dev/general-theiagen/staphb/srst2:0.2.0-vcholerae"
     Int disk_size = 100
     Int cpu = 4
@@ -32,11 +32,11 @@ task srst2_vibrio {
       ${INPUT_READS} \
       --gene_db /vibrio-cholerae-db/vibrio_230224.fasta \
       --output ~{samplename} \
-      --min_coverage ~{srst2_min_cov} \
-      --max_divergence ~{srst2_max_divergence} \
-      --min_depth ~{srst2_min_depth} \
-      --min_edge_depth ~{srst2_min_edge_depth} \
-      --gene_max_mismatch ~{srst2_gene_max_mismatch}
+      --min_coverage ~{min_cov} \
+      --max_divergence ~{max_divergence} \
+      --min_depth ~{min_depth} \
+      --min_edge_depth ~{min_edge_depth} \
+      --gene_max_mismatch ~{gene_max_mismatch}
     
     # capture output TSV
     mv ~{samplename}__genes__*__results.txt ~{samplename}.tsv
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index eea239514..d27986762 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -516,7 +516,7 @@
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
       md5sum: 9b8e2da62c8572a369c786a9bbc3a36e
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: 3c9c727d4a40ca936f58446103becb34
+      md5sum: 3547638e39dcf408234a6c1df57d198d
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
       contains: ["version", "QC", "output"]
     - path: miniwdl_run/workflow.log
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index deaab812c..017d07868 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -487,7 +487,7 @@
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
       md5sum: 02dc0075bf28d557d7b81aa2dc61feab
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: 3c9c727d4a40ca936f58446103becb34
+      md5sum: 3547638e39dcf408234a6c1df57d198d
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
       md5sum: 09d9f68b9ca8bf94b6145ff9bed2edd1
     - path: miniwdl_run/workflow.log
diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
index f264970aa..de6e5e340 100644
--- a/workflows/utilities/wf_merlin_magic.wdl
+++ b/workflows/utilities/wf_merlin_magic.wdl
@@ -610,11 +610,11 @@ workflow merlin_magic {
           read1 = select_first([read1]),
           read2 = read2,
           samplename = samplename,
-          srst2_min_cov = srst2_min_cov,
-          srst2_max_divergence = srst2_max_divergence,
-          srst2_min_depth = srst2_min_depth,
-          srst2_min_edge_depth = srst2_min_edge_depth,
-          srst2_gene_max_mismatch = srst2_gene_max_mismatch,
+          min_cov = srst2_min_cov,
+          max_divergence = srst2_max_divergence,
+          min_depth = srst2_min_depth,
+          min_edge_depth = srst2_min_edge_depth,
+          gene_max_mismatch = srst2_gene_max_mismatch,
           docker = srst2_docker_image
       }
     }