diff --git a/README.md b/README.md index 400c374..a50119d 100644 --- a/README.md +++ b/README.md @@ -38,6 +38,7 @@ Below is a simplified diagram to illustrate the design logic and functionalities

+ 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: diff --git a/docs/output.md b/docs/output.md index ca5152a..c89760e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -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: @@ -751,7 +751,7 @@ Above means Singularity will be used and jobs will be submitted via LSF. 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: @@ -787,7 +787,7 @@ Above means Singularity will be used and jobs will be submitted via LSF. 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