Merge pull request #103 from MaxUlysse/patch

fix issue with downloading star-fusion references
nf-core · Feb 10, 2020 · 505a0fb · 505a0fb
2 parents 227cf0c + e8320fa
commit 505a0fb
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/download-references.nf b/download-references.nf
@@ -117,7 +117,7 @@ process download_arriba {
     script:
     """
     wget -N https://github.com/suhrig/arriba/releases/download/v1.1.0/arriba_v1.1.0.tar.gz -O arriba_v1.1.0.tar.gz
-    tar -xvzf arriba_v1.1.0.tar.gz && mv arriba_v1.1.0/database/* . && gunzip * && rm -rf arriba_*
+    tar -xvzf arriba_v1.1.0.tar.gz && mv arriba_v1.1.0/database/* . && gunzip *.gz && rm -rf arriba_*
     """
 }
 

diff --git a/download-singularity-img.nf b/download-singularity-img.nf
@@ -57,13 +57,13 @@ if (params.help) exit 0, helpMessage()
 params.running_tools = ["nf-core/rnafusion/${workflow.manifest.version}"]
 if (!params.outdir) exit 1, "Output directory not specified!"
 
-if (params.arriba || download_all) params.running_tools.add("Arriba")
-if (params.star_fusion || download_all) params.running_tools.add("STAR-Fusion")
-if (params.fusioncatcher || download_all) params.running_tools.add("Fusioncatcher")
-if (params.ericscript || download_all) params.running_tools.add("Ericscript")
-if (params.pizzly || download_all) params.running_tools.add("Pizzly")
-if (params.squid || download_all) params.running_tools.add("Squid")
-if (params.fusion_inspector || download_all) params.running_tools.add("Fusion-Inspector")
+if (params.arriba || params.download_all) params.running_tools.add("Arriba")
+if (params.star_fusion || params.download_all) params.running_tools.add("STAR-Fusion")
+if (params.fusioncatcher || params.download_all) params.running_tools.add("Fusioncatcher")
+if (params.ericscript || params.download_all) params.running_tools.add("Ericscript")
+if (params.pizzly || params.download_all) params.running_tools.add("Pizzly")
+if (params.squid || params.download_all) params.running_tools.add("Squid")
+if (params.fusion_inspector || params.download_all) params.running_tools.add("Fusion-Inspector")
 
 // Header log info
 log.info nfcoreHeader()