From df60a58426705cc9feb6850f69b42f00f383df8c Mon Sep 17 00:00:00 2001
From: Lasse Folkersen <lassefolkersen@gmail.com>
Date: Wed, 16 Mar 2022 13:29:11 +0100
Subject: [PATCH] round the < to ( to make markdown work for meta.yml (#1395)

* round the < to ( to make markdown work for meta.yml

* changing md5sums and stub output so it doesnt trigger the empty file linting error
---
 modules/ascat/main.nf        | 18 +++++++++---------
 modules/ascat/meta.yml       | 22 +++++++++++-----------
 tests/modules/ascat/test.yml | 18 +++++++++---------
 3 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/modules/ascat/main.nf b/modules/ascat/main.nf
index 1d2bd96f..35f262dd 100644
--- a/modules/ascat/main.nf
+++ b/modules/ascat/main.nf
@@ -137,15 +137,15 @@ process ASCAT {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.cnvs.txt
-    touch ${prefix}.purityploidy.txt
-    touch ${prefix}.segments.txt
-    touch Tumour.ASCATprofile.png
-    touch Tumour.ASPCF.png
-    touch Tumour.germline.png
-    touch Tumour.rawprofile.png
-    touch Tumour.sunrise.png
-    touch Tumour.tumour.png
+    echo stub > ${prefix}.cnvs.txt
+    echo stub > ${prefix}.purityploidy.txt
+    echo stub > ${prefix}.segments.txt
+    echo stub > Tumour.ASCATprofile.png
+    echo stub > Tumour.ASPCF.png
+    echo stub > Tumour.germline.png
+    echo stub > Tumour.rawprofile.png
+    echo stub > Tumour.sunrise.png
+    echo stub > Tumour.tumour.png
 
     echo 'ASCAT:' > versions.yml
     echo ' ascat: 3.0.0' >> versions.yml
diff --git a/modules/ascat/meta.yml b/modules/ascat/meta.yml
index 949afd6a..b44862a1 100644
--- a/modules/ascat/meta.yml
+++ b/modules/ascat/meta.yml
@@ -15,23 +15,23 @@ input:
   - args:
       type: map
       description: |
-        Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. <optional> parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
+        Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
 
         ```
         {
           [
             "gender": "XX",
             "genomeVersion": "hg19"
-            "purity": <optional>,
-            "ploidy": <optional>,
-            "gc_files": <optional>,
-            "minCounts": <optional>,
-            "chrom_names": <optional>,
-            "min_base_qual": <optional>,
-            "min_map_qual": <optional>,
-            "ref_fasta": <optional>,
-            "skip_allele_counting_tumour": <optional>,
-            "skip_allele_counting_normal": <optional>
+            "purity": (optional),
+            "ploidy": (optional),
+            "gc_files": (optional),
+            "minCounts": (optional),
+            "chrom_names": (optional),
+            "min_base_qual": (optional),
+            "min_map_qual": (optional),
+            "ref_fasta": (optional),
+            "skip_allele_counting_tumour": (optional),
+            "skip_allele_counting_normal": (optional)
           ]
         }
         ```
diff --git a/tests/modules/ascat/test.yml b/tests/modules/ascat/test.yml
index e46c66b4..668e8823 100644
--- a/tests/modules/ascat/test.yml
+++ b/tests/modules/ascat/test.yml
@@ -4,22 +4,22 @@
     - ascat
   files:
     - path: output/ascat/Tumour.ASCATprofile.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/Tumour.ASPCF.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/Tumour.germline.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/Tumour.rawprofile.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/Tumour.sunrise.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/Tumour.tumour.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/test.cnvs.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/test.purityploidy.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/test.segments.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
     - path: output/ascat/versions.yml
       md5sum: 1af20694ec11004c4f8bc0c609b06386