# 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 @@ - - + + + + + + + + + + + + + @@ -113,4 +132,4 @@ - \ No newline at end of file +