Onboarding Ruitong

[lpantano]

Access to resources:

• O2 and O2 on demand
• Seqera.io
• bcbioR repository

Onboarding on technology:

• Platform webpage
• Going over https://training.nextflow.io/hello_nextflow/ to catch up on nextflow
• ATACseq

First work:

• nextflow_schema.json in nf-core ATACseq pipeline: create a parameter that allows selecting size fragments. New parameter needs to be added to nextflow.log, as well to nextflow_schema.json. If parameter is given, it will add options here: https://github.com/nf-core/atacseq/blob/dev/conf/modules.config#L465 as:

args = '--ATACshift --minFragmentLength 0 --maxFragmentLength 120 '

Example of adding parameters when options are on or off or with value is here.

• single cell MAST in bcbioR. Validate code with test example data. Alex should be able to help to point to the example data. Draft code in O2 is at: /n/data1/cores/bcbio/platform/development/templates_drafts (mast.R and mast_template.R). Both files should be located in a new folder at the single cell template folder. The readme should be update to mention this new template.

[lijin0303]

I forked the original git repo's dev branch and then created a new branch on my forked repo called ruitong_dev. I implemented the size fragment selection option as highlighted in this commit based on my current understanding. Please let me know if anything looks confusing or incorrect. Thanks!

[lpantano]

Add this to the documentation for other regions to consider:

ATACRanges = {"NF": ATACRange("NF", 0, 100),
"MN": ATACRange("MN", 180, 247),
"DN": ATACRange("DN", 315, 473),
"TN": ATACRange("TN", 558, 615)}