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Kai Hu committed Jun 25, 2022
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -38,6 +38,7 @@ Below is a simplified diagram to illustrate the design logic and functionalities
<p align="center">
<img src="docs/images/scATACpipe_workflow.svg" width="500" style="display: block; margin: 20px auto">
</p>

The main functionalities of each sub-workflow are summarized below. You can also refer to the [output - Result folders](https://github.com/hukai916/scATACpipe/blob/main/docs/output.md#result-folders) for more details.

#### PREPROCESS_DEFAULT:
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6 changes: 3 additions & 3 deletions docs/output.md
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Expand Up @@ -720,7 +720,7 @@ Above means Singularity will be used and jobs will be submitted via LSF.

Pipeline info is saved at [./test_data1_default_homo_sapiens/pipeline_info](https://github.com/hukai916/scATACpipe_example/tree/main/test_data1_default_homo_sapiens/pipeline_info).

A final report is saved at [./test_data1_default_homo_sapiens/multiqc/multiqc_report.html](https://rawcdn.githack.com/hukai916/scATACpipe_example/2f396d2abcfcedd902bee4e6b9cb8674e2181d57/test_data1_default_homo_sapiens/multiqc/multiqc_report.html)
A final report is saved at [./test_data1_default_homo_sapiens/multiqc/multiqc_report.html](https://rawcdn.githack.com/hukai916/scATACpipe_example/f73e37944477b65a2ed80556a10a335c9c99212c/test_data1_default_homo_sapiens/multiqc/multiqc_report.html)

#### Example2: default preprocessing with hg38 (UCSC)
Command used:
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Pipeline info is saved at [./test_data1_default_hg38/pipeline_info](https://github.com/hukai916/scATACpipe_example/tree/main/test_data1_default_hg38/pipeline_info).

A final report is saved at [./test_data1_default_hg38/multiqc/multiqc_report.html](https://rawcdn.githack.com/hukai916/scATACpipe_example/2f396d2abcfcedd902bee4e6b9cb8674e2181d57/test_data1_default_hg38/multiqc/multiqc_report.html)
A final report is saved at [./test_data1_default_hg38/multiqc/multiqc_report.html](https://rawcdn.githack.com/hukai916/scATACpipe_example/f73e37944477b65a2ed80556a10a335c9c99212c/test_data1_default_hg38/multiqc/multiqc_report.html)

#### Example3: preprocessing with Chromap using hg38 (UCSC)
Command used:
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Pipeline info is saved at [./test_data1_chromap_hg38/pipeline_info](https://github.com/hukai916/scATACpipe_example/tree/main/test_data1_chromap_hg38/pipeline_info).

A final report is saved at [./test_data1_chromap_hg38/multiqc/multiqc_report.html](https://rawcdn.githack.com/hukai916/scATACpipe_example/2f396d2abcfcedd902bee4e6b9cb8674e2181d57/test_data1_chromap_hg38/multiqc/multiqc_report.html)
A final report is saved at [./test_data1_chromap_hg38/multiqc/multiqc_report.html](https://rawcdn.githack.com/hukai916/scATACpipe_example/f73e37944477b65a2ed80556a10a335c9c99212c/test_data1_chromap_hg38/multiqc/multiqc_report.html)

## Pipeline information
<details markdown="1">
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