2 changed files with 1 additions and 5 deletions
+ 0
- 3
tasks/samtools.wdl
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| String bam = base + ".bam" | String bam = base + ".bam" | ||||
| String sorted_bam = base + ".sorted.bam" | String sorted_bam = base + ".sorted.bam" | ||||
| String sorted_bam_index = base + ".sorted.bam.bai" | String sorted_bam_index = base + ".sorted.bam.bai" | ||||
| String viral_samstats = base + ".viral.samstats" | |||||
| String docker | String docker | ||||
| String cluster | String cluster | ||||
| /opt/conda/bin/samtools view -bS ${sam} > ${bam} | /opt/conda/bin/samtools view -bS ${sam} > ${bam} | ||||
| /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 stats ${sorted_bam} > ${viral_samstats} | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| output { | output { | ||||
| File out_bam = sorted_bam | File out_bam = sorted_bam | ||||
| File out_bam_index = sorted_bam_index | File out_bam_index = sorted_bam_index | ||||
| File out_viral_samstats = viral_samstats | |||||
| } | } | ||||
| } | } |
+ 1
- 2
workflow.wdl
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| File read1 | File read1 | ||||
| File read2 | File read2 | ||||
| File idx | |||||
| File idx | |||||
| String idx_prefix | String idx_prefix | ||||
| File gtf | |||||
| call hisat2.hisat2 as hisat2 { | call hisat2.hisat2 as hisat2 { |
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