fq3 can be null

README.md

@@ -10,13 +10,21 @@
 ```
 $ source activate choppy-pipe-0.3.8.dev0
 $ choppy install songyueqiang/mergefq
+# 如果已安装，可加参数 -f
+$ choppy install songyueqiang/mergefq -f
 $ choppy apps
 ```
 
 #### quick start
 
 ```
+# 运行命令
 $ choppy batch songyueqiang/mergefq-latest sample.csv --project-name Your_project_name
+# 查询运行情况
+$ choppy query -s ID 
+# 查询报错信息
+$ choppy query -s ID -m
+
 ```
 
 

sample.csv

@@ -1,2 +1,2 @@
-sample_id,fq_list,disk_size,fq_m
-mergefq,oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R1_400k.gz;oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R2_400k.gz,10,Quartet_RNA_ILM_NovaSeq.fastq.gz
+sample_id,fq1,fq2,fq3,disk_size,fq_m
+mergefq,oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R1_400k.gz,oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R2_400k.gz,,10,Quartet_RNA_ILM_NovaSeq.fastq.gz

tasks/mergefq.wdl

@@ -8,7 +8,11 @@ task mergefq {
 
 	command <<<
 		set -euo pipefail
+		if [ ! ${fq3} ]; then
+		cat ${fq1} ${fq2} > ${fq_m}
+		else
 	    cat ${fq1} ${fq2} ${fq3} > ${fq_m}
+		fi
 	>>>
 
 	runtime {

workflow.wdl

@@ -13,7 +13,7 @@ workflow {{ project_name }} {
 			fq1=fq1,
 			fq2=fq2,
 			fq3=fq3,
-			fq_m=fq_m
+			fq_m=fq_m,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 	}