# HG changeset patch
# User dvanzessen
# Date 1587469105 0
# Node ID 7d5b46d41ff00ec70e61e23b1109165df6d30016
# Parent b766a897b902cf760c56a0f7c3a8ccc73e8164d1
Uploaded
diff -r b766a897b902 -r 7d5b46d41ff0 bcbio-nextgen.xml
--- a/bcbio-nextgen.xml Thu Feb 27 14:25:51 2020 +0000
+++ b/bcbio-nextgen.xml Tue Apr 21 11:38:25 2020 +0000
@@ -8,7 +8,11 @@
--bed ${region_file.bed}
#end if
#for $i, $sample in enumerate( $samples )
- --input $sample.forward:$sample.reverse:$sample.phenotype
+ #if str( $sample.single_or_paired.single_or_paired_selector ) == "single":
+ --input $sample.single_or_paired.forward:$sample.phenotype
+ #else:
+ --input $sample.single_or_paired.forward:$sample.single_or_paired.reverse:$sample.phenotype
+ #end if
#end for
&& bcbio_nextgen.py \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml -t local -n \$BCBIO_CORES &&
zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf &&
@@ -30,7 +34,11 @@
analysis: $analysis
lane: {{ loop.index }}
description: {{ sample['description'] }}
+{% if 'reverse' in sample %}
files: [{{ sample['forward'] }}, {{ sample['reverse'] }}]
+{% else %}
+ files: [{{ sample['forward'] }}]
+{% endif %}
genome_build: $build
metadata:
phenotype: {{ sample['phenotype'] }}
@@ -93,8 +101,19 @@
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@@ -113,4 +132,4 @@
-
\ No newline at end of file
+