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

Added new module for Toulligqc #5131

Merged
merged 27 commits into from
Mar 28, 2024
Merged

Added new module for Toulligqc #5131

merged 27 commits into from
Mar 28, 2024

Conversation

Salome-Brunon
Copy link
Contributor

@Salome-Brunon Salome-Brunon commented Mar 15, 2024 •
edited
Loading

ToulligQC is a post sequencing QC tool for Oxford Nanopore sequencers. This nf-core module is quite basic but we aim to implement a few more options in the near future!

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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@Salome-Brunon Salome-Brunon requested a review from a team as a code owner March 15, 2024 14:28
@Salome-Brunon Salome-Brunon requested review from CarsonJM and removed request for a team March 15, 2024 14:28
@Salome-Brunon Salome-Brunon reopened this Mar 15, 2024
@Salome-Brunon
Copy link
Contributor Author

@nf-core-bot fix linting

FriederikeHanssen
FriederikeHanssen reviewed Mar 19, 2024
View reviewed changes
modules/nf-core/toulligqc/main.nf Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/main.nf Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/main.nf Outdated Show resolved Hide resolved
Salome-Brunon and others added 7 commits March 19, 2024 09:40
@Salome-Brunon @FriederikeHanssen
Update modules/nf-core/toulligqc/meta.yml
1b07601 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@Salome-Brunon @FriederikeHanssen
Update modules/nf-core/toulligqc/meta.yml
d3e6d86 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@Salome-Brunon @FriederikeHanssen
Update modules/nf-core/toulligqc/meta.yml
8f78d86 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@Salome-Brunon @FriederikeHanssen
Update modules/nf-core/toulligqc/main.nf
4310cd3 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@Salome-Brunon
Merge branch 'toulligqc' of github.com:Salome-Brunon/modules into tou…
f8e3db5 
…lligqc
@Salome-Brunon
UPDATE: added fastq as input option
67eaf13
@Salome-Brunon
Merge branch 'master' into toulligqc
f891afb
jfy133
jfy133 reviewed Mar 26, 2024
View reviewed changes
modules/nf-core/toulligqc/main.nf Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/main.nf Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/tests/main.nf.test Outdated Show resolved Hide resolved
Salome-Brunon and others added 2 commits March 26, 2024 14:25
@Salome-Brunon @jfy133
Update modules/nf-core/toulligqc/meta.yml
486a54c 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@Salome-Brunon @jfy133
Update modules/nf-core/toulligqc/meta.yml
4557e5d 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@Salome-Brunon Salome-Brunon requested a review from jfy133 March 26, 2024 15:03
@Salome-Brunon Salome-Brunon requested a review from jfy133 March 27, 2024 11:16
jfy133
jfy133 reviewed Mar 27, 2024
View reviewed changes
Copy link
Member

@jfy133 jfy133 left a comment •
edited
Loading

Choose a reason for hiding this comment

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

See comment below... Sorry about this. Shouldn't be doing this while travelling 😅

modules/nf-core/toulligqc/main.nf Show resolved Hide resolved
@Salome-Brunon Salome-Brunon requested a review from jfy133 March 28, 2024 10:02
jfy133
jfy133 reviewed Mar 28, 2024
View reviewed changes
Copy link
Member

@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

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

Ok I'm working today before holiday, so looking through more properly now :D

modules/nf-core/toulligqc/main.nf Outdated
Comment on lines 11 to 13
tuple val(meta), path(seq_summary)
tuple val(meta), path(fastq)
tuple val(meta), path(bam)
Copy link
Member

Choose a reason for hiding this comment

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

Suggested change
tuple val(meta), path(seq_summary)
tuple val(meta), path(fastq)
tuple val(meta), path(bam)
tuple val(meta), path(seq_summary), path(fastq), path(bam)

modules/nf-core/toulligqc/main.nf Outdated Show resolved Hide resolved
modules/nf-core/toulligqc/tests/main.nf.test

}

test("sarscov2 - nanopore bam") {
Copy link
Member

Choose a reason for hiding this comment

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

Can you add one test with all three if they are not mutually exclusive

Copy link
Contributor Author

Choose a reason for hiding this comment

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

I can do but I will need to upload new data to the nf-core/tets-datasets repo as I don't think the sequencing summary, FASTQ and BAM files come from the same run..

Copy link
Member

Choose a reason for hiding this comment

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

Ah ok, that would be a bit awkward... maybe you could do a local test and otherwise I avert my eyes ;)

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Okay thank you! I'll do a local test this afternoon and will let you know the outcome :)

Copy link
Contributor Author

@Salome-Brunon Salome-Brunon Mar 28, 2024 •
edited
Loading

Choose a reason for hiding this comment

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

I have done a test with a sequencing summary and fastq file and it worked!
I don't have access to a bam file right now but there is no reason for it not to work :)
local_test_seq_summary_fastq

@Salome-Brunon Salome-Brunon requested a review from jfy133 March 28, 2024 12:53
jfy133
jfy133 approved these changes Mar 28, 2024
View reviewed changes
Copy link
Member

@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

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

You can merge! Thanks for your patience!

@Salome-Brunon
Copy link
Contributor Author

@jfy133 Thank you for all the help!
Only issue is that I don't have the rights to merge the pull request 😅 Could you do it? Thanks!

@Salome-Brunon Salome-Brunon requested a review from jfy133 March 28, 2024 14:20
@jfy133
Copy link
Member

jfy133 commented Mar 28, 2024

Oh! Then please request joining the nf-core orgnisation here: https://nf-co.re/join#github and you will get merge rights :) I will merge for you!

@jfy133 jfy133 added this pull request to the merge queue Mar 28, 2024
Merged via the queue into nf-core:master with commit 49423bb Mar 28, 2024
11 checks passed
jvfe added a commit that referenced this pull request Mar 28, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
2d824ce 
* master:
  Added new module for Toulligqc (#5131)
  Make `mosdepth` stub use `gzip` for `.gz` files (#5410)
  Update hmmsearch to 3.4 (#5408)
  port `controlfreec-makegraph` to nf-test (#5393)
  port `controlfreec-freec` to nf-test (#5398)
  port `controlfreec-assesssignificance` to nf-test (#5396)
  port `controlfreec-makegraph2` to nf-test (#5392)
  new module: crabz (#5351)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@CarsonJM CarsonJM Awaiting requested review from CarsonJM CarsonJM was automatically assigned from nf-core/nf-test

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

@jfy133 jfy133 Awaiting requested review from jfy133

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

Successfully merging this pull request may close these issues.
5 participants
@Salome-Brunon @jfy133 @FriederikeHanssen @nf-core-bot @pinin4fjords