1 changed files with 3 additions and 3 deletions
+ 3
- 3
tasks/arriba.wdl
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| --genomeLoad NoSharedMemory \ | --genomeLoad NoSharedMemory \ | ||||
| --readFilesIn ${fastq1} ${fastq2} \ | --readFilesIn ${fastq1} ${fastq2} \ | ||||
| --readFilesCommand zcat \ | --readFilesCommand zcat \ | ||||
| --outStd BAM_Unsorted \ | |||||
| --outSAMtype BAM Unsorted \ | --outSAMtype BAM Unsorted \ | ||||
| --outSAMunmapped Within \ | --outSAMunmapped Within \ | ||||
| --outBAMcompression 0 \ | --outBAMcompression 0 \ | ||||
| --chimScoreJunctionNonGTAG 0 \ | --chimScoreJunctionNonGTAG 0 \ | ||||
| --chimScoreSeparation 1 \ | --chimScoreSeparation 1 \ | ||||
| --chimSegmentReadGapMax 3 \ | --chimSegmentReadGapMax 3 \ | ||||
| --chimMultimapNmax 50 > ./output/${sample_id}.Aligned.out.bam | |||||
| --chimMultimapNmax 50 \ | |||||
| --outFileNamePrefix ./output/${sample_id} | |||||
| /arriba_v2.1.0/arriba \ | /arriba_v2.1.0/arriba \ | ||||
| -x ./output/${sample_id}.Aligned.out.bam \ | |||||
| -x ./output/${sample_id}Aligned.out.bam \ | |||||
| -o ./output/${sample_id}_fusions.tsv -O ./output/${sample_id}_fusions.discarded.tsv \ | -o ./output/${sample_id}_fusions.tsv -O ./output/${sample_id}_fusions.discarded.tsv \ | ||||
| -a ${ASSEMBLY_FA} \ | -a ${ASSEMBLY_FA} \ | ||||
| -g ${ANNOTATION_GTF} \ | -g ${ANNOTATION_GTF} \ |
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