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@@ -25,22 +25,22 @@ We recommend using choppy system and Aliyun OSS service. The command will look l |
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```Shell |
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# Activate the choppy environment |
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open-choppy-env |
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$open-choppy-env |
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# Install the APP |
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choppy install YaqingLiu/variant-calling-latest [-f] |
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$choppy install YaqingLiu/variant-calling-latest [-f] |
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# List the parameters |
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choppy samples YaqingLiu/variant-calling-latest [--no-default] |
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$choppy samples YaqingLiu/variant-calling-latest [--no-default] |
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# Submit you task with the `samples.csv file` and `project name` |
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choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label] |
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$choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label] |
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# Query the status of all tasks in the project |
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choppy query -L Label | grep "status" |
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$choppy query -L Label | grep "status" |
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``` |
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**Please note**: The `defaults` can be forcibly replaced by the settings in `samples.csv`. Therefore, there is no need to contact me over this issue. |
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**Please note:** The `defaults` can be forcibly replaced by the settings in `samples.csv`. Therefore, there is no need to contact me over this issue. |
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The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2 |
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