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stead99
8ceecb10b7
change GENE_ID to gene_id in ballgown task
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4 年之前 | |
|---|---|---|
| conf | 4 年之前 | |
| tasks | 4 年之前 | |
| README.md | 4 年之前 | |
| defaults | 4 年之前 | |
| inputs | 4 年之前 | |
| manifest.json | 4 年之前 | |
| schema.json | 4 年之前 | |
| workflow.wdl | 4 年之前 | |
README.md
Author: Jun Shang
Email: shangjunv@163.com
Last Updates: 29/06/2020
Requirements
- choppy
- Ali-Cloud
$ source activate choppy/open-choppy-env
$ choppy install junshang/rnaseq-engineering:tag
$ choppy apps
quick start
$ choppy samples junshang/rnaseq-engineering:tag > samples.csv
$ choppy batch junshang/rnaseq-engineering:tag samples.csv -p Your_project_name
The samplec.csv looks like this:
| sample_id | disk_size | read1 | read2 | pre_alignment_qc | qualimap_qc | trim_adapter |
|---|---|---|---|---|---|---|
| FDU_D5 | 200 | 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 | false | true | true |
- sample_id： 一般设置为文件输出前缀
- read1： R1 fastq 文件所在路径
- read2： R2 fastq 文件所在路径
- disk_size： 磁盘空间，每一步中间文件大小做调整
- pre_alignment_qc: 执行 fastqc 和 fastq screen 设置为 true，反之设置为 false
- qualimap_qc: 执行 qualimap bamqc 设置为 true，反之设置为 false
- trim_adapter: 使用 fastp 去 adapter 设置为 true，反之设置为 false
参考文献
APP 主要来自于 Quartet RNA-seq 标准流程