Mercurial > repos > davidvanzessen > shm_csr

changeset 89:3c9d4d976c47 draft

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"planemo upload commit 8b702d0cf8f2355307eb8f95989f3d2488b2c963"
author rhpvorderman
date Fri, 05 Nov 2021 13:41:03 +0000
parents a84ac3ee87e1
children 6809c63d9161
files shm_csr.xml wrapper.sh
diffstat 2 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/shm_csr.xml	Wed Oct 27 12:32:21 2021 +0000
+++ b/shm_csr.xml	Fri Nov 05 13:41:03 2021 +0000
@@ -1,5 +1,5 @@
-<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.2.1">
-	<description>Performs a summary/analysis of an IMGT HighV-QUEST (https://www.imgt.org/HighV-QUEST/) ZIP file for Somatic hypermutation and class switch recombination.</description>
+<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.3.0">
+	<description></description>
 	<requirements>
 		<requirement type="package" version="3.7.1">python</requirement>
 		<requirement type="package" version="0.4.4">changeo</requirement>
@@ -16,8 +16,6 @@
 		<requirement type="package" version="4.4.18">bash</requirement>
 		<requirement type="package" version="1.34">tar</requirement>
 		<requirement type="package" version="5.39">file</requirement>
-		<container type="docker">quay.io/rhpvorderman/mulled-v2-a2524529ff4c0254c944ff4606e926ca2e8b80d0:9fa3e7fda79c80bf1af596872bddd871913a2c1c-0</container>
-		<container type="singularity">docker://quay.io/rhpvorderman/mulled-v2-a2524529ff4c0254c944ff4606e926ca2e8b80d0:9fa3e7fda79c80bf1af596872bddd871913a2c1c-0</container>
 	</requirements>
 	<command interpreter="bash">
 		#if str ( $filter_unique.filter_unique_select ) == "remove":
--- a/wrapper.sh	Wed Oct 27 12:32:21 2021 +0000
+++ b/wrapper.sh	Fri Nov 05 13:41:03 2021 +0000
@@ -895,12 +895,12 @@
 echo "---------------- remove_files----------------"
 echo "---------------- remove_files----------------<br />" >> $log
 
-rm -r -v results/baseline
-rm -r -v files
+rm -r -v -f results/baseline
+rm -r -v -f files
 filename='remove_files.txt'
 
 while read file; do
-    rm -v $file
+    rm -v -f $file
 done < "$filename"