add files

README.md

@@ -0,0 +1,20 @@
+> Author: Yueqiang Song
+> Email: songyq_hello@163.com
+> Last Updates: 25/12/2020
+
+#### Requirements
+
+- choppy
+- Ali-Cloud
+
+```
+$ source activate choppy-pipe-0.3.8.dev0
+$ choppy install songyueqiang/mergefq
+$ choppy apps
+```
+
+#### quick start
+
+```
+$ choppy batch songyueqiang/mergefq-latest sample.csv --project-name Your_project_name
+```

sample.csv

@@ -0,0 +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

tasks/mergefq.wdl

@@ -6,7 +6,7 @@ task mergefq {
 
 	command <<<
 		set -euo pipefail
-		IFS=";" read -a myarray <<< ${fq_list} 
+		IFS=";" read -a myarray <<< ${fq_list}		
         cat ${myarray[@]} >${fq_m}
 		
 	>>>