1 changed files with 1 additions and 1 deletions
+ 1
- 1
tasks/stringtie.wdl
View File
| @@ -13,7 +13,7 @@ task stringtie { | |||
| command <<< | |||
| nt=$(nproc) | |||
| mkdir ballgown | |||
| /opt/conda/bin/stringtie -e -B -p $nt -f ${minimum_isoform_abundance} -m ${minimum_length_allowed_for_the_predicted_transcripts} -a ${Junctions_no_spliced_reads} -M ${maximum_fraction_of_muliplelocationmapped_reads} -G ${gtf} -o ballgown/${sample_id}/${sample_id}.gtf -C ${sample_id}.cov.ref.gtf -A ${sample_id}.gene.abundance.txt ${bam} | |||
| /opt/conda/bin/stringtie -e -B -p $nt -f ${minimum_isoform_abundance} -m ${minimum_length_allowed_for_the_predicted_transcripts} -a ${Junctions_no_spliced_reads} -M ${maximum_fraction_of_muliplelocationmapped_reads} -G ${gtf} --rf -o ballgown/${sample_id}/${sample_id}.gtf -C ${sample_id}.cov.ref.gtf -A ${sample_id}.gene.abundance.txt ${bam} | |||
| >>> | |||
Loading…