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choppy samples --no-default chenqingwang/SplAdder-merge-latest > samples.csv |
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choppy samples --no-default chenqingwang/SplAdder-merge-latest > samples.csv |
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# 提交任务 |
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# 提交任务 |
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$ choppy batch chenqingwang/SplAdder-merge-latest samples.csv -p Your_project_name -l Your_label |
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$ choppy batch chenqingwang/SplAdder-merge-latest samples.json -p Your_project_name -l Your_label |
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# 查询任务运行状况 |
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# 查询任务运行状况 |
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$ choppy query -L Your_label | grep "status" |
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$ choppy query -L Your_label | grep "status" |
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# 结果文件地址 |
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# 结果文件地址 |
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$ oss://choppy-cromwell-result/test-choppy/Your_project_name/ |
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$ oss://choppy-cromwell-result/test-choppy/Your_project_name/ |
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``` |
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``` |
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#### Input File |
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Input file samples.json should be in the form of json. For example: |
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``` |
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{ |
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"bam": [ |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.bam", |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.bam", |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.bam" |
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], |
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"bai": [ |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.bai", |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.bai", |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.bai" |
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], |
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"pickle": [ |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.pickle", |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.pickle", |
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"oss://choppy-cromwell-result/test-choppy/..._xxx.pickle" |
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], |
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"sample_id": "B13150xx" |
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} |
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``` |
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PS: sample_id is necessary for Choppy system |