revised-bedtools-task

README.md

@@ -17,11 +17,11 @@ $ choppy apps
 
 #### 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

input_samples.csv

@@ -0,0 +1,2 @@
+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

tasks/bedtools.wdl

@@ -9,8 +9,10 @@ task bedtools {
 	String disk_size
 
 	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 
 	
 	>>>