``` | ``` | ||||
$ source activate choppy-pipe-0.3.8.dev0 | $ source activate choppy-pipe-0.3.8.dev0 | ||||
$ choppy install songyueqiang/mergefq | $ choppy install songyueqiang/mergefq | ||||
# 如果已安装,可加参数 -f | |||||
$ choppy install songyueqiang/mergefq -f | |||||
$ choppy apps | $ choppy apps | ||||
``` | ``` | ||||
#### quick start | #### quick start | ||||
``` | ``` | ||||
# 运行命令 | |||||
$ choppy batch songyueqiang/mergefq-latest sample.csv --project-name Your_project_name | $ 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_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 |
command <<< | command <<< | ||||
set -euo pipefail | set -euo pipefail | ||||
if [ ! ${fq3} ]; then | |||||
cat ${fq1} ${fq2} > ${fq_m} | |||||
else | |||||
cat ${fq1} ${fq2} ${fq3} > ${fq_m} | cat ${fq1} ${fq2} ${fq3} > ${fq_m} | ||||
fi | |||||
>>> | >>> | ||||
runtime { | runtime { |
fq1=fq1, | fq1=fq1, | ||||
fq2=fq2, | fq2=fq2, | ||||
fq3=fq3, | fq3=fq3, | ||||
fq_m=fq_m | |||||
fq_m=fq_m, | |||||
disk_size=disk_size, | disk_size=disk_size, | ||||
cluster_config=cluster_config | cluster_config=cluster_config | ||||
} | } |