diff --git a/README.md b/README.md index 3ceb17334edd0153006cc483eea113b91ab5b4c7..3be132add5e564245493866d6165cb0f80d9c753 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ BICF ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-s The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. -This pipeline is primarily used with a SLURM cluster on the [BioHPC Cluster](https://biohpc.swmed.edu/). However, the pipeline should be able to run on any system that Nextflow supports. +This pipeline is primarily used with a SLURM cluster on the [BioHPC Cluster](https://portal.biohpc.swmed.edu/content/). However, the pipeline should be able to run on any system that Nextflow supports. Additionally, the pipeline is designed to work with [Astrocyte Workflow System](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html) using a simple web interface. @@ -46,6 +46,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git + See [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/test_data/design_ENCSR729LGA_PE.txt) for an example design file, paired-end + + See [HERE](test_data/design_ENCSR729LGA_PE.txt) for an example design file, paired-end + See [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/test_data/design_ENCSR238SGC_SE.txt) for an example design file, single-end ##### 3) Bash Script