From c452f562890534ca3d0a331de7c35b744037fdae Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 25 May 2022 12:29:14 +0000
Subject: [PATCH] Patch mash screen

---
 modules/mash/screen/main.nf        |  8 ++++----
 modules/mash/screen/meta.yml       |  9 +++++----
 tests/modules/mash/screen/main.nf  |  9 ++++++---
 tests/modules/mash/screen/test.yml | 10 +++++-----
 4 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/modules/mash/screen/main.nf b/modules/mash/screen/main.nf
index 3e7859ed..be272cbb 100644
--- a/modules/mash/screen/main.nf
+++ b/modules/mash/screen/main.nf
@@ -8,8 +8,8 @@ process MASH_SCREEN {
         'quay.io/biocontainers/mash:2.3--he348c14_1' }"
 
     input:
-    tuple val(meta), path(query_sketch)
-    path fastx_db
+    tuple val(meta), path(query)
+    path sequences_sketch
 
     output:
     tuple val(meta), path("*.screen"), emit: screen
@@ -26,8 +26,8 @@ process MASH_SCREEN {
         screen \\
         $args \\
         -p $task.cpus \\
-        $query_sketch \\
-        $fastx_db \\
+        $sequences_sketch \\
+        $query \\
         > ${prefix}.screen
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/mash/screen/meta.yml b/modules/mash/screen/meta.yml
index 81e455bc..063aca6c 100644
--- a/modules/mash/screen/meta.yml
+++ b/modules/mash/screen/meta.yml
@@ -20,13 +20,14 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - query_sketch:
+  - query:
       type: file
-      description: MinHash sketch of query sequences
-      pattern: "*.msh"
-  - fastx_db:
+      description: Query sequences
+      pattern: "*.fastq.gz"
+  - sequence_sketch:
       type: file
       description: Sequence files to match against
+      pattern: "*.msh"
 
 output:
   - meta:
diff --git a/tests/modules/mash/screen/main.nf b/tests/modules/mash/screen/main.nf
index 7f0b8bd9..5338d932 100644
--- a/tests/modules/mash/screen/main.nf
+++ b/tests/modules/mash/screen/main.nf
@@ -14,8 +14,11 @@ workflow test_mash_screen {
             file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
         ]
     ]
-    fastx_db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    sars_db = [
+        [ id: 'sars_db' ],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
 
-    MASH_SKETCH ( input )
-    MASH_SCREEN ( MASH_SKETCH.out.mash, fastx_db )
+    MASH_SKETCH ( sars_db )
+    MASH_SCREEN ( input, MASH_SKETCH.out.mash.map { meta, sketch -> sketch } )
 }
diff --git a/tests/modules/mash/screen/test.yml b/tests/modules/mash/screen/test.yml
index f622817a..e4907ce9 100644
--- a/tests/modules/mash/screen/test.yml
+++ b/tests/modules/mash/screen/test.yml
@@ -4,9 +4,9 @@
     - mash
     - mash/screen
   files:
-    - path: output/mash/test.mash_stats
-      md5sum: 2a6f297d8e69a5e4160243bc6c89129c
-    - path: output/mash/test.msh
-      md5sum: d747145a43dad5f82342036f8f5d9133
+    - path: output/mash/sars_db.mash_stats
+      md5sum: 1dafbd23e36e18bf4c87a007d0fc98f7
+    - path: output/mash/sars_db.msh
+      md5sum: 24289e4a13526e88eeb2abfca4a0f0a8
     - path: output/mash/test.screen
-      md5sum: d3c871dccd5cd57ab54781fa5c5d7278
+      md5sum: ac8701e1aab651b2f36c6380b1351b11