Adding plasflow module #3555

limrp · 2023-06-24T21:37:20Z

A new module for the cram-size command of the samtools tool has been added.

modules/nf-core/samtools/cramsize/main.nf

tests/modules/nf-core/samtools/cramsize/test.yml

nvnieuwk · 2023-06-29T12:25:39Z

Very good job already! Here are some comments to make this module adhere to the guidelines set up by nf-core. Feel free to ping me if you have any questions

Adding name of the tool Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Adding prefix to make the module set up more flexible. Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Changing `.baseName` by `prefix` in output names. Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

- Stub section added to main.nf script. - test.yml file added to module samtools/cramsize

nvnieuwk · 2023-07-10T08:04:19Z

Hi some tests are still failing, can you fix these before I do a final review? Also it's easier to get reviews when you have one module per PR (don't worry about it for now, just some advice for the future 😉)

limrp · 2023-07-28T00:54:10Z

Hi some tests are still failing, can you fix these before I do a final review? Also it's easier to get reviews when you have one module per PR (don't worry about it for now, just some advice for the future wink)

Thank you for checking! I'll review the test that are failing 😃
Sorry for the 2 modules in one PR. I'll be more careful in the future 🥲 😺

* Update manta somatic * Update manta tumoronly

* add call subcommand * at calls runs now [skip ci] * add test files * linting * fix tests * add contains check * Update tests/modules/nf-core/varlociraptor/callvariants/main.nf Co-authored-by: Maxime U Garcia <[email protected]> --------- Co-authored-by: Maxime U Garcia <[email protected]>

* add module template * first version * update testing and linting * update file naming * update test * fix test

* ngmerge first commit * main module code * complete module * remove trailing whitespace * fix versions.yml * fix version yml * versions yml * vyml * try vyml again * touch versions yml * vyml

* initial commit * module version 1 * full testing * linting * fix version yaml * fix version yaml command * fix version yml maybe this time please * fix version yml for real this time * try again versions yaml * fix version yml * vyml * version yaml * vyml * update ref to have meta

Co-authored-by: Steven Strong <[email protected]>

Fix metaeuk and add tests

* add -f option * update tests

* new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * update vardictjava

plasflow module

…ule.

limrp · 2023-09-27T19:34:39Z

Tests for plasflow are still failing if you fixed those I'll give you a ✔️ :p

Hi @nvnieuwk !
The only tests that are failing are the ones related to Plasflow from Conda. There is no issue with Plasflow from Docker and Singularity. There is also no problem with Samtools' cramsize.

I attempted to fix Plasflow's recipe in the Bioconda repository. I needed to specify the required Python version (3.5) for Plasflow to function.

Here is the link: bioconda/bioconda-recipes#42697

However, I was given the following message:

DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
ERROR: tensorflow-0.10.0rc0-cp35-cp35m-linux_x86_64.whl is not a supported wheel on this platform.

It seems that it will not be possible to make Plasflow work with conda because conda will not support Python 3.5 soon. But everything else works fine.
Do you think that in a case like this is it possible to accept the PR?

nvnieuwk · 2023-09-28T06:59:02Z

Can you add the tool to be excluded from the conda tests in .github/workflows/test.yml? You'll see it in the pytest clause. This way conda won't be tested (this should only be used for tools that absolutely don't work with conda though). After that all tests should pass and you'll be ready to go. Thanks for all the effort in trying to fix it

limrp · 2023-09-28T13:46:47Z

Can you add the tool to be excluded from the conda tests in .github/workflows/test.yml? You'll see it in the pytest clause. This way conda won't be tested (this should only be used for tools that absolutely don't work with conda though). After that all tests should pass and you'll be ready to go. Thanks for all the effort in trying to fix it

Hi @nvnieuwk ! Thanks for your reply!

Are you refering to this section of the test.yml file?

Should I add Plasflow to that list?

Thanks a lot for all you advice!

nvnieuwk · 2023-09-28T13:50:06Z

Yes, that's it!

SPPearce · 2024-08-16T08:34:36Z

I'm going to close this for now, as there seems to be no response from @limrp .
I moved the samtools cramsize module out into a separate PR and merged that, but I can't immediately see a way to get plasflow to work properly

limrp added 2 commits June 24, 2023 16:10

New module for the cram-size command of samtools.

13c52e9

"Adding module for cram-size command of the samtools tool"

9d24d79

limrp marked this pull request as draft June 24, 2023 21:38

limrp marked this pull request as ready for review June 24, 2023 21:54

limrp changed the title ~~Adding module for cram-size command of the samtools tool~~ Adding module for cram-size command of samtools Jun 24, 2023

Merge branch 'master' into master

d64477f

nvnieuwk reviewed Jun 29, 2023

View reviewed changes

priyanka-surana self-requested a review June 30, 2023 15:12

limrp and others added 10 commits July 6, 2023 12:31

Update modules/nf-core/samtools/cramsize/main.nf

65b3a9a

Adding name of the tool Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Update modules/nf-core/samtools/cramsize/main.nf

99c3260

Adding prefix to make the module set up more flexible. Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Update modules/nf-core/samtools/cramsize/main.nf

20c1d63

Changing `.baseName` by `prefix` in output names. Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Stub added to the main.nf script.

43fa886

Adding generated test.yml file.

dda123d

Merge branch 'master' of https://github.com/nf-core/modules

62af573

Updating my master branch with the changes made in cramsize-branch:

7506ff9

- Stub section added to main.nf script. - test.yml file added to module samtools/cramsize

Adding pytest.

e80fa18

Adding a new nf-core module called plasflow.

afda96d

Merging branch with new module plasflow

7b0714f

maxulysse and others added 9 commits July 28, 2023 01:33

Update manta modules (nf-core#3615)

e6aebc5

* Update manta somatic * Update manta tumoronly

add new module iCount-mini/metagene (nf-core#3612)

9f28ebe

* add module template * first version * update testing and linting * update file naming * update test * fix test

Newmodule ngmerge (nf-core#3626)

9a7a2ec

* ngmerge first commit * main module code * complete module * remove trailing whitespace * fix versions.yml * fix version yml * versions yml * vyml * try vyml again * touch versions yml * vyml

fix integer overflow (nf-core#3620)

c69b9ca

Co-authored-by: Steven Strong <[email protected]>

Fix metaeuk_easypredict when using mmseqs database (nf-core#3525)

c7e83fa

Fix metaeuk and add tests

3630 add unstitched reads as emitted output of ngmerge (nf-core#3632)

40a29ea

* add -f option * update tests

Update vardictjava (nf-core#3633)

b971c6a

* new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * update vardictjava

limrp added 10 commits July 31, 2023 10:09

Merge branch 'pf' with latest change about the conda environment for

d73b1c9

plasflow module

Adding specific Tensorflow version for Plasflow.

99edf70

Merge branch 'pf' with Tensorflow version in conda environment.

b9199b7

Adding channel for python 3.5

eeb8cba

Merge remote-tracking branch 'upstream/master'

beb5d82

Merge branch 'pf' with channel for python 3.5 specified

5d1f7d1

Fixing the channel for python 3.5 for plasflow module.

31d0b5d

Merge branch 'pf'

05337f4

Changing the channel for python 3.5 (to conda-forge) for plasflow mod…

78e7c83

…ule.

Merge branch 'pf'

5f8751a

edmundmiller requested a review from a team as a code owner October 19, 2023 16:26

edmundmiller requested a review from sateeshperi October 19, 2023 16:26

SPPearce and others added 4 commits April 30, 2024 06:06

Merge branch 'master' into master

bdb7df9

Merge branch 'master' into master

dedbeac

Update cramsize

4407fb4

Excluse cramsize from pytest

e630347

SPPearce mentioned this pull request Jun 3, 2024

Add samtools cramsize #5743

Merged

17 tasks

Merge branch 'master' into master

be0e4c4

SPPearce changed the title ~~Adding module for cram-size command of samtools~~ Adding plasflow module Jun 4, 2024

SPPearce added 3 commits June 4, 2024 15:49

Delete modules/nf-core/samtools/cramsize_old/main.nf

39f9030

Delete modules/nf-core/samtools/cramsize_old/meta.yml

38347b0

Update environment.yml

3459a65

SPPearce marked this pull request as draft June 12, 2024 10:37

SPPearce added the stale Stale label Aug 13, 2024

SPPearce closed this Aug 16, 2024

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Adding plasflow module #3555

Adding plasflow module #3555

limrp commented Jun 24, 2023

nvnieuwk commented Jun 29, 2023

nvnieuwk commented Jul 10, 2023

limrp commented Jul 28, 2023 •

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limrp commented Sep 27, 2023

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nvnieuwk commented Sep 28, 2023

SPPearce commented Aug 16, 2024

Adding plasflow module #3555

Adding plasflow module #3555

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nvnieuwk commented Sep 28, 2023

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