LUYAO REN
6 years ago
1 changed files with 2 additions and 3 deletions
+ 2
- 3
tasks/mapping.wdl
View File
| STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix OnePass_ | STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix OnePass_ | ||||
| genomeDir=./twoPass | |||||
| STAR --runMode genomeGenerate --genomeDir $genomeDir --genomeFastaFiles ${STref_dir}/${fasta} --sjdbFileChrStartEnd OnePass_SJ.out.tab --sjdbOverhang 75 --runThreadN 12 | |||||
| STAR --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles ${STref_dir}/${fasta} --sjdbFileChrStartEnd OnePass_SJ.out.tab --sjdbOverhang 75 --runThreadN 12 | |||||
| STAR --genomeDir $genomeDir --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_ | |||||
| STAR --genomeDir ./ --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_ | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
Loading…