Mercurial > repos > kkonganti > hfp_nowayout

diff hfp_nowayout.xml @ 10:74ac6f6a9526 tip

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planemo upload
author kkonganti
date Tue, 01 Apr 2025 11:08:01 -0400
parents 5734210632d8
children
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line diff
--- a/hfp_nowayout.xml	Tue Apr 01 10:27:56 2025 -0400
+++ b/hfp_nowayout.xml	Tue Apr 01 11:08:01 2025 -0400
@@ -48,8 +48,8 @@
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	-profile gxkubernetes;
-    mv './cpipes-output/nowayout-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
-    mv './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' './CPIPES_nowayout_krona.html' || exit 1;
+    mv './cpipes-output/nowayout-multiqc/CPIPES-Report_multiqc_report.html' './multiqc_report.html' || exit 1;
+    if [ -e './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' ]; then mv './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' './CPIPES_nowayout_krona.html'; else echo '<html><h1>No mitochondrial reads detected in any of the samples</h1></html>' > './CPIPES_nowayout_krona.html'; fi;
     rm -rf ./cpipes-output || exit 1;
     rm -rf ./work || exit 1;
     ]]></command>