From 4317ad85aede53086cdb1ac2410a46e85e00bed4 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Fri, 29 Apr 2022 15:07:32 +0200
Subject: [PATCH] Passing test

---
 modules/sexdeterrmine/main.nf               |  2 ++
 tests/modules/sexdeterrmine/main.nf         |  2 +-
 tests/modules/sexdeterrmine/nextflow.config |  6 +++++-
 tests/modules/sexdeterrmine/test.yml        | 21 ++++++++++++---------
 4 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/modules/sexdeterrmine/main.nf b/modules/sexdeterrmine/main.nf
index f8754764..dd8b5a70 100644
--- a/modules/sexdeterrmine/main.nf
+++ b/modules/sexdeterrmine/main.nf
@@ -23,6 +23,8 @@ process SEXDETERRMINE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
+    if ("$depth" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
     sexdeterrmine \\
         -I $depth \\
diff --git a/tests/modules/sexdeterrmine/main.nf b/tests/modules/sexdeterrmine/main.nf
index c9d869f5..2c90d280 100644
--- a/tests/modules/sexdeterrmine/main.nf
+++ b/tests/modules/sexdeterrmine/main.nf
@@ -9,7 +9,7 @@ workflow test_sexdeterrmine {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ]
+        file("https://github.com/nf-core/test-datasets/raw/eager/testdata/Human/bam/JK2067_downsampled_s0.1.bam", checkIfExists: true) ]
 
     SAMTOOLS_DEPTH ( input )
     SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
diff --git a/tests/modules/sexdeterrmine/nextflow.config b/tests/modules/sexdeterrmine/nextflow.config
index 763d7ad6..4ba3dfe3 100644
--- a/tests/modules/sexdeterrmine/nextflow.config
+++ b/tests/modules/sexdeterrmine/nextflow.config
@@ -3,6 +3,10 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName:SAMTOOLS_DEPTH {
-        ext.args = "-aa -H"
+        ext.args = "-H"
+    }
+
+    withName:SEXDETERRMINE {
+        ext.prefix = { "${meta.id}_sexdet" }
     }
 }
diff --git a/tests/modules/sexdeterrmine/test.yml b/tests/modules/sexdeterrmine/test.yml
index 5eca8a30..54c471ba 100644
--- a/tests/modules/sexdeterrmine/test.yml
+++ b/tests/modules/sexdeterrmine/test.yml
@@ -1,12 +1,15 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml sexdeterrmine
-- name: "sexdeterrmine"
-  command: nextflow run ./tests/modules/sexdeterrmine -entry test_sexdeterrmine -c ./tests/config/nextflow.config -c ./tests/modules/sexdeterrmine/nextflow.config
+- name: sexdeterrmine test_sexdeterrmine
+  command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config
   tags:
-    - "sexdeterrmine"
-    #
+    - sexdeterrmine
   files:
-    - path: "output/sexdeterrmine/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/samtools/test.tsv
+      md5sum: c894abd0c78ea7760e0b54bbafb93722
+    - path: output/samtools/versions.yml
+      md5sum: dbd04b700335c8ad236bd667254c8dd8
+    - path: output/sexdeterrmine/sexdeterrmine.json
+      md5sum: 16d9e7891d4c92bc1d66db2e70e9d86f
+    - path: output/sexdeterrmine/test_sexdet.tsv
+      md5sum: 7ffc35e478de66939819a9ca4a5df2d7
     - path: output/sexdeterrmine/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+      md5sum: 077361101e8e7997aec3da8a01e59eee