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fq3 can be null

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songyq 4 年之前
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共有 4 個檔案被更改,包括 15 行新增3 行删除
  1. +8
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      README.md
  2. +2
    -2
      sample.csv
  3. +4
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      tasks/mergefq.wdl
  4. +1
    -1
      workflow.wdl

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README.md 查看文件

``` ```
$ 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

``` ```





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sample.csv 查看文件

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

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tasks/mergefq.wdl 查看文件



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 {

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workflow.wdl 查看文件

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
} }

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