Zhihui
4 years ago
2 changed files with 3 additions and 3 deletions
+ 2
- 2
tasks/samtools.wdl
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| /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam} | /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam} | ||||
| /opt/conda/bin/samtools index ${sorted_bam} | /opt/conda/bin/samtools index ${sorted_bam} | ||||
| /opt/conda/bin/samtools view -bs 42.1 ${sorted_bam} > ${percent_bam} | /opt/conda/bin/samtools view -bs 42.1 ${sorted_bam} > ${percent_bam} | ||||
| /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${sample_id}.ins_size | |||||
| #/opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${sample_id}.ins_size | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| File out_bam = sorted_bam | File out_bam = sorted_bam | ||||
| File out_percent = percent_bam | File out_percent = percent_bam | ||||
| File out_bam_index = sorted_bam_index | File out_bam_index = sorted_bam_index | ||||
| File out_ins_size = ins_size | |||||
| #File out_ins_size = ins_size | |||||
| } | } | ||||
| } | } |
+ 1
- 1
workflow.wdl
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| gene_abundance = stringtie.gene_abundance, | gene_abundance = stringtie.gene_abundance, | ||||
| count_length = count_length | count_length = count_length | ||||
| } | } | ||||
| } | |||||
| } |
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