New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Metagenomics Illumina Nextflow conversion: Now runs checkm separately on every bin #134

Open

olabiyi wants to merge 6 commits into nasa:DEV_Metagenomics_Illumina_NF_conversion from olabiyi:DEV_Metagenomics_Illumina_NF_conversion

olabiyi commented Jan 14, 2025

I made the following changes:

Renamed the input csv file parameter from --csv_file to --input_file.
Edited the README and help message to reflect this change.
Split checkm runs by bin in the processing solving the recursion error generated by checkm when too many bins are generated by the workflow .
Added sanity checks for the required workflow input parameters.

olabiyi added 6 commits

January 14, 2025 08:35


          Now running checkm separately on every bin

d0a7654


          Fixed typo in config

7e2b178


          Updated the nextflow version

fb7ab75


          Changed the default value of accession

72f9321


          update ampillumina pipelined document

50f1f8c


          Added launchDir variable

e028bcd

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet