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tasks/hisat2.wdl
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| @@ -17,7 +17,7 @@ task hisat2 { | |||
| command <<< | |||
| nt=$(nproc) | |||
| hisat2 -t -p $nt -x ${idx}/${idx_prefix} --pen-cansplice ${pen_cansplice} --pen-noncansplice ${pen_noncansplice} --pen-intronlen ${pen_intronlen} --min-intronlen ${min_intronlen} --max-intronlen ${max_intronlen} --maxins ${maxins} --minins ${minins} --un-conc-gz ${sample_id}_un.fq.gz -1 ${Trim_R1} -2 ${Trim_R2} -S ${sample_id}.sam | |||
| hisat2 -t -p $nt -x ${idx}/${idx_prefix} --pen-cansplice ${pen_cansplice} --pen-noncansplice ${pen_noncansplice} --pen-intronlen ${pen_intronlen} --min-intronlen ${min_intronlen} --max-intronlen ${max_intronlen} --maxins ${maxins} --minins ${minins} --rna-strandness RF --un-conc-gz ${sample_id}_un.fq.gz -1 ${Trim_R1} -2 ${Trim_R2} -S ${sample_id}.sam | |||
| >>> | |||
| runtime { | |||
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