Skip to content
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.

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

Increase trinity resources #16

Merged
merged 3 commits into from
Oct 25, 2024
Merged

Conversation

avani-bhojwani
Copy link
Collaborator

@avani-bhojwani avani-bhojwani commented Oct 25, 2024

Increased resources for the Trinity module as this step often times out. This addresses Issue #12.

Trinity documentation suggests that for 1 M pairs of Illumina reads, you would need 1GB of memory and 0.5-1hr of time.
For estimation purposes, based on samples on NCBI's SRA, I would say 1 sample=~30M paired reads. To make an assembly from 6 samples, 180GB memory and 90-180 hrs would seem like a reasonable amount of resources to try out.

PR checklist

  • This comment contains a description of changes (with reason).
  • [N/A] If you've fixed a bug or added code that should be tested, add tests!
  • [N/A] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/denovotranscript branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • [N/A] Usage Documentation in docs/usage.md is updated.
  • [N/A] Output Documentation in docs/output.md is updated.
  • [N/A] CHANGELOG.md is updated.
  • [N/A] README.md is updated (including new tool citations and authors/contributors).

@avani-bhojwani avani-bhojwani merged commit a9443de into dev Oct 25, 2024
5 checks passed
@avani-bhojwani avani-bhojwani deleted the increase_trinity_resources branch October 25, 2024 03:45
@avani-bhojwani avani-bhojwani mentioned this pull request Oct 25, 2024
5 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant