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.

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

Adds lint config to ignore some tests (linting) #5

Open
wants to merge 19 commits into
base: master
Choose a base branch
from
Open

Adds lint config to ignore some tests (linting) #5

wants to merge 19 commits into from

Conversation

cgpu
Copy link
Collaborator

@cgpu cgpu commented Mar 24, 2021

Check here, introduced recently with nf-core tools > v1.13
https://nf-co.re/tools#linting-config

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

cgpu and others added 19 commits March 24, 2021 23:17
@cgpu
Adds .nf-core-lint.yml and inits nf-core lint tests to False (#4)
3bc2bbf 
Check here, introduced recently with nf-core tools > v1.13
https://nf-co.re/tools#linting-config
@cgpu
Adds main.pbs and slurm config
6faea30
@cgpu
Config as param
d3b4679
@cgpu
Adds google.config
9da4ae7
@cgpu
Bumps minimum disk from 10.GB to 30.GB
baf814b 
I was having a lot of error 3 @sk-sahu, I think the minimum per VM is 30.GB as we have in CloudOS.
Will double check and revisit, for now bumping to 30GB to check the hypothesis.
@cgpu
Adds local.config
5b37ae8
@cgpu
Adds local config
8c1be33
@cgpu
Adds required projectDir = workflow.projectDir
81bf962
@sk-sahu @cgpu
updates cpu and memory to base
42d2b42
@cgpu
Updates cpus
5cac65e
@sk-sahu @cgpu
Update base.config
d745633
@cgpu
Adds errorStrategy as params [default: terminate]
40c25c5
@cgpu
Skips by default [documentation,versions]
972cc0e
@cgpu
Workaround for projectDir in 20.01
b950efb
@cgpu
Update v.NF to 20.01 in ci.yml; Adds fail-fast false
25c9271
@cgpu
Adds conditional to not attempt to build redundant channels
aa54aa9
@cgpu
Adds conditional, !validate redundant process channels
6dc3c31
@cgpu
Sets Haplotype caller minimum heap to 4.GB (4000m)
7a2c7ef
@cgpu
Bumps sungle cpu mem to 2.GB
0779e82 
Because of this error:
https://cloudos.lifebit.ai/public/jobs/605c5de4cc2b27011245d5f9

  Execution failed: allocating: creating instance: inserting instance: Invalid value for field 'resource.machineType': 'zones/us-east1-b/machineTypes/custom-16-10240'. Memory size for 16.0 vCPU instance should be between 14848MiB and 106496MiB, while 10240MiB is requested.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@cgpu @sk-sahu