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

Release 1.0.1 - Minor template update release #41

Merged
merged 48 commits into from
Apr 26, 2024
Merged

Release 1.0.1 - Minor template update release #41

merged 48 commits into from
Apr 26, 2024

Conversation

a4000
Copy link
Contributor

@a4000 a4000 commented Mar 26, 2024

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 - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/readsimulator 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>).
  • 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).

nf-core-bot and others added 30 commits February 20, 2024 15:29
Important! Template update for nf-core/tools v2.13.1
Added option for using draft genomes with insilicoseq
@a4000 a4000 mentioned this pull request Mar 27, 2024
11 tasks
Comment on lines 14 to 15
run: |
curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
run: |
curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
run: |
echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT

A small oversight in the last template release, this is from the current dev branch, to make this action actually work

a4000 and others added 2 commits April 15, 2024 13:46
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
added pattern to ncbidownload_group to allow a comma separated list of groups
Copy link
Contributor

@SPPearce SPPearce left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good to me, just a few minor things.

main.nf Outdated
// Validate input parameters
if (params.validate_params) {
validateParameters()
// TODO nf-core: Remove this line if you don't need a FASTA file
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

TODO still here

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should note that multiqc version has changed 1.19 -> 1.21

CHANGELOG.md Outdated
@@ -3,7 +3,20 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.0.0 - 2024-02-07
## 1.0.1 - 2024-03-22
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
## 1.0.1 - 2024-03-22
## 1.0.1 - 2024-03-23

modules/local/insilicoseq/generate/main.nf Outdated Show resolved Hide resolved
a4000 and others added 4 commits April 26, 2024 12:23
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Changes based on PR #41 reviews
@a4000 a4000 merged commit 0e8805d into master Apr 26, 2024
23 of 24 checks passed
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.

5 participants