From c3687ef54bc0f651ea332c228317baf34c643c18 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <mail@gregor-sturm.de>
Date: Tue, 28 Sep 2021 21:25:10 +0200
Subject: [PATCH] fix more ver yml (#757)

* Fix featurecounts

* whitespace change to trigger CI on yara/mapper

* update test yaml
---
 modules/subread/featurecounts/main.nf        |  2 +-
 tests/modules/subread/featurecounts/test.yml | 18 +++++++++---------
 tests/modules/yara/mapper/main.nf            |  4 ++--
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/subread/featurecounts/main.nf b/modules/subread/featurecounts/main.nf
index 3e2eb765..76209a0d 100644
--- a/modules/subread/featurecounts/main.nf
+++ b/modules/subread/featurecounts/main.nf
@@ -49,7 +49,7 @@ process SUBREAD_FEATURECOUNTS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(featureCounts -v 2>&1 | sed -e "s/featureCounts v//g")
+        ${getSoftwareName(task.process)}: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
     END_VERSIONS
     """
 }
diff --git a/tests/modules/subread/featurecounts/test.yml b/tests/modules/subread/featurecounts/test.yml
index 2cba9e15..be6bed47 100644
--- a/tests/modules/subread/featurecounts/test.yml
+++ b/tests/modules/subread/featurecounts/test.yml
@@ -4,10 +4,10 @@
     - subread
     - subread/featurecounts
   files:
-    - path: output/subread/test.featureCounts.txt.summary
-      md5sum: d78617192451a57f6ef249ddcaf13720
     - path: output/subread/test.featureCounts.txt
-      md5sum: b0a1f7563afe49007f422d4c9ca5ee6c
+      md5sum: 0012df4c0a0e47eec1440017ab34f75f
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 8f602ff9a8ef467af43294e80b367cdf
 
 - name: subread featurecounts test_subread_featurecounts_reverse
   command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config
@@ -15,10 +15,10 @@
     - subread
     - subread/featurecounts
   files:
-    - path: output/subread/test.featureCounts.txt.summary
-      md5sum: 4217004d0b55f870f77092364f59e44d
     - path: output/subread/test.featureCounts.txt
-      md5sum: 412840a8880cd29674b3d5404d3de19b
+      md5sum: 8175816b8260ed444d59232bd7e7120b
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 7cfa30ad678b9bc1bc63afbb0281547b
 
 - name: subread featurecounts test_subread_featurecounts_unstranded
   command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config
@@ -26,7 +26,7 @@
     - subread
     - subread/featurecounts
   files:
-    - path: output/subread/test.featureCounts.txt.summary
-      md5sum: ee585faeb1edfcd2188a5e486a0e98a9
     - path: output/subread/test.featureCounts.txt
-      md5sum: 6b684e11a1e54bec7e1ee5e3f651d7fd
+      md5sum: 3307d31b44a5d6bb3389786bb8f4e91f
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 23164b79f9f23f11c82820db61a35560
diff --git a/tests/modules/yara/mapper/main.nf b/tests/modules/yara/mapper/main.nf
index 06582eb3..9cdce40d 100644
--- a/tests/modules/yara/mapper/main.nf
+++ b/tests/modules/yara/mapper/main.nf
@@ -3,8 +3,8 @@
 nextflow.enable.dsl = 2
 
 
-include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams( options: ['args': '-e 3'] )
-include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf' addParams( options: ['args': '-e 3'] )
+include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams(options: ['args': '-e 3'])
+include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf' addParams(options: ['args': '-e 3'])
 
 workflow test_yara_single_end {