Loading modules.json +1 −1 Original line number Diff line number Diff line Loading @@ -19,7 +19,7 @@ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "bowtie2/align": { "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773" "git_sha": "61f68913fefc20241ceccb671b104230b2d775d7" }, "bowtie2/build": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" Loading modules/nf-core/modules/bowtie2/align/main.nf +4 −0 Original line number Diff line number Diff line Loading @@ -29,6 +29,8 @@ process BOWTIE2_ALIGN { def unaligned = 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 @@ -49,6 +51,8 @@ process BOWTIE2_ALIGN { def unaligned = 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.json +1 −1 Original line number Diff line number Diff line Loading @@ -19,7 +19,7 @@ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "bowtie2/align": { "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773" "git_sha": "61f68913fefc20241ceccb671b104230b2d775d7" }, "bowtie2/build": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" Loading
modules/nf-core/modules/bowtie2/align/main.nf +4 −0 Original line number Diff line number Diff line Loading @@ -29,6 +29,8 @@ process BOWTIE2_ALIGN { def unaligned = 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 @@ -49,6 +51,8 @@ process BOWTIE2_ALIGN { def unaligned = 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
