Loading modules/nf-core/modules/bowtie2/align/main.nf +6 −0 Original line number Diff line number Diff line Loading @@ -34,6 +34,9 @@ process BOWTIE2_ALIGN { def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'` [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1 bowtie2 \\ -x \$INDEX \\ -U $reads \\ Loading @@ -54,6 +57,9 @@ process BOWTIE2_ALIGN { def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'` [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1 bowtie2 \\ -x \$INDEX \\ -1 ${reads[0]} \\ Loading Loading
modules/nf-core/modules/bowtie2/align/main.nf +6 −0 Original line number Diff line number Diff line Loading @@ -34,6 +34,9 @@ process BOWTIE2_ALIGN { def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'` [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1 bowtie2 \\ -x \$INDEX \\ -U $reads \\ Loading @@ -54,6 +57,9 @@ process BOWTIE2_ALIGN { def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'` [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1 bowtie2 \\ -x \$INDEX \\ -1 ${reads[0]} \\ Loading
