LUYAO REN
6 jaren geleden
1 gewijzigde bestanden met toevoegingen van 2 en 2 verwijderingen
+ 2
- 2
tasks/mapping.wdl
Bestand weergeven
| @@ -15,13 +15,13 @@ task mapping { | |||
| set -o pipefail | |||
| set -e | |||
| STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --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 20 | |||
| STAR --genomeDir $genomeDir --readFilesIn ${fastq_1} ${fastq_2} --runThreadN 20 --outFileNamePrefix ${sample}_ | |||
| STAR --genomeDir $genomeDir --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_ | |||
| >>> | |||
| runtime { | |||
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