3 ha cambiato i file con 9 aggiunte e 5 eliminazioni
+ 3
- 3
README.md
Vedi File
| #### quick start | #### quick start | ||||
| 1. 将 input_samples.tsv 放到阿里云，路径用户自己设定 | |||||
| - 将 input_samples.tsv 放到阿里云，路径用户自己设定 | |||||
| > input_samples_file.tsv 格式参考上述示例文件 | |||||
| > input_samples_file.tsv 格式参考上述示例文件 | |||||
| 2. 准备 samples.csv 文件，如下： | |||||
| - 准备 samples.csv 文件，如下： | |||||
| ``` | ``` | ||||
| $ choppy samples junshang/bedtools-latest > samples.csv | $ choppy samples junshang/bedtools-latest > samples.csv |
+ 2
- 0
input_samples.csv
Vedi File
| oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/43061775-40e6-47e7-8f07-b961b44c596f/call-samtools/GCCACATA_S9_L001_R1_001.sorted.bam oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/43061775-40e6-47e7-8f07-b961b44c596f/call-samtools/GCCACATA_S9_L001_R1_001.sorted.bam.bai | |||||
| oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/49bd025e-5275-4fbd-9e67-b279b08ce8b5/call-samtools/F1_S6_L001_R1_001.sorted.bam oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/49bd025e-5275-4fbd-9e67-b279b08ce8b5/call-samtools/F1_S6_L001_R1_001.sorted.bam.bai |
+ 4
- 2
tasks/bedtools.wdl
Vedi File
| String disk_size | String disk_size | ||||
| command <<< | command <<< | ||||
| bedtools multicov -bams ${bam} -bed ${bed_file} > revread_count.txt | |||||
| mkdir -p /cromwell_root/tmp/bedtools | |||||
| cp ${bam} ${bai} /cromwell_root/tmp/bedtools | |||||
| cd /cromwell_root/tmp/bedtools | |||||
| bedtools multicov -bams GCCACATA_S9_L001_R1_001.sorted.bam F1_S6_L001_R1_001.sorted.bam -bed ${bed_file} > revread_count.txt | |||||
| >>> | >>> | ||||
Loading…