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

Add mapping tools and viral pathogen List #21

Merged
merged 25 commits into from
Jul 22, 2024
Merged

Add mapping tools and viral pathogen List #21

merged 25 commits into from
Jul 22, 2024

Conversation

LilyAnderssonLee
Copy link
Collaborator

@LilyAnderssonLee LilyAnderssonLee commented Jun 18, 2024 •
edited
Loading

Add mapping tools: bowtie2 for short reads and minimap2 for long reads.
Fix #19 #20 #22

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 genomic-medicine-sweden/meta-val 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).

@LilyAnderssonLee LilyAnderssonLee requested a review from a team as a code owner June 18, 2024 13:50
@github-actions GitHub Actions
Copy link

github-actions bot commented Jun 18, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9346870

+| ✅ 161 tests passed       |+
#| ❔ 177 tests were ignored |#
!| ❗  16 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-18 12:58:51

@LilyAnderssonLee LilyAnderssonLee changed the title Add mapping tools Add mapping tools and viral pathogen List Jun 18, 2024
sofstam
sofstam reviewed Jun 24, 2024
View reviewed changes
nextflow_schema.json Outdated Show resolved Hide resolved
viral_pathogen_List.csv Outdated Show resolved Hide resolved
.nf-core.yml Outdated Show resolved Hide resolved
sofstam
sofstam reviewed Jul 18, 2024
View reviewed changes
conf/modules.config Show resolved Hide resolved
conf/modules.config Outdated Show resolved Hide resolved
conf/modules.config Show resolved Hide resolved
conf/modules.config Show resolved Hide resolved
conf/modules.config Show resolved Hide resolved
nextflow_schema.json Outdated Show resolved Hide resolved
nextflow_schema.json Outdated Show resolved Hide resolved
nextflow_schema.json Outdated Show resolved Hide resolved
nextflow_schema.json Outdated Show resolved Hide resolved
workflows/metaval.nf Show resolved Hide resolved
LilyAnderssonLee and others added 13 commits July 18, 2024 13:37
@LilyAnderssonLee @sofstam
Update conf/modules.config
17e72b6 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update conf/modules.config
484429b 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update conf/modules.config
22aa86a 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update conf/modules.config
6a5e515 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update nextflow_schema.json
3b912c7 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update nextflow_schema.json
b19db4f 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update nextflow_schema.json
7b1b179 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update nextflow_schema.json
c2cc381 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee
Trail whitespace
eac76ca
@LilyAnderssonLee
move the multiqc to the end of modules.config
bed5faa
@LilyAnderssonLee @sofstam
Update nextflow_schema.json
d16c390 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update nextflow.config
36cc422 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee @sofstam
Update nextflow_schema.json
9346870 
Co-authored-by: Sofia Stamouli <[email protected]>
sofstam
sofstam approved these changes Jul 22, 2024
View reviewed changes
Copy link
Contributor

@sofstam sofstam left a comment

Choose a reason for hiding this comment

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

🌟

@LilyAnderssonLee LilyAnderssonLee merged commit 5ad9b2a into dev Jul 22, 2024
4 checks passed
@LilyAnderssonLee LilyAnderssonLee deleted the mapping branch October 15, 2024 13:11
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@sofstam sofstam sofstam approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Add bowtie2/minimap2 to perform mapping
2 participants
@LilyAnderssonLee @sofstam