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tasks/teprof_s1.wdl
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| --outSAMtype BAM SortedByCoordinate \ | --outSAMtype BAM SortedByCoordinate \ | ||||
| --outFileNamePrefix ./${sample_id}. | --outFileNamePrefix ./${sample_id}. | ||||
| samtools view -@ 8 -q 255 -h ${sample_id}.Aligned.sortedByCoord.out.bam > ${sample_id}.filtered.Aligned.sortedByCoord.out.bam | |||||
| samtools view -@ 16 -q 255 -h ${sample_id}.Aligned.sortedByCoord.out.bam > ${sample_id}.filtered.Aligned.sortedByCoord.out.bam | |||||
| stringtie -p 8 ${sample_id}.filtered.Aligned.sortedByCoord.out.bam -o ${sample_id}.Aligned.sortedByCoord.out.gtf -m 100 -c 1 --rf | stringtie -p 8 ${sample_id}.filtered.Aligned.sortedByCoord.out.bam -o ${sample_id}.Aligned.sortedByCoord.out.gtf -m 100 -c 1 --rf | ||||
| python /database/rnapipelinerefhg38/rnapipeline/rmskhg38_annotate_gtf_update_test_tpm.py ${sample_id}.Aligned.sortedByCoord.out.gtf /database/rnapipelinerefhg38/rnapipeline/arguments.txt | python /database/rnapipelinerefhg38/rnapipeline/rmskhg38_annotate_gtf_update_test_tpm.py ${sample_id}.Aligned.sortedByCoord.out.gtf /database/rnapipelinerefhg38/rnapipeline/arguments.txt | ||||
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