Add kmcp classifier #312

sofstam · 2023-06-27T09:38:21Z

This PR closes #210

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/taxprofiler 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>).
Usage Documentation in docs/usage.md is updated.
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CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2023-06-27T09:40:11Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit e5df2f9

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

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Run details

nf-core/tools version 2.9
Run at 2023-08-19 08:44:30

sofstam · 2023-07-20T15:58:41Z

@jfy133 I have added the KMCP_COMPUTE in the profiling workflow. I get an error for KMCP_INDEX:
intput and output paths should not be the same

In the module test, this was adressed with:

https://github.com/nf-core/modules/blob/master/tests/modules/nf-core/kmcp/index/nextflow.config

I am not sure how this should be implemented here. Shall I create a new def new_meta ?

Co-authored-by: James A. Fellows Yates <[email protected]>

jfy133 · 2023-08-15T15:44:55Z

You've installed KMCP merge but it's not used anywhere, is that correct? I would be expecting this in standardisation_profiles.nf and modules.conf if so.

I will update the metromap diagram next review :)

I forgot to remove the module, updating the PR now.

What does merge do exactly though? Multiple samples profiles in one? That would be useful!

It is merge results from different databases.

jfy133

I may and try implement the remaining changes myself now if I have time

CHANGELOG.md

docs/output.md

docs/usage.md

subworkflows/local/profiling.nf

Co-authored-by: James A. Fellows Yates <[email protected]>

jfy133

LGTM, thanks for the patience @sofstam ! That was a complicated one!

Start adding kmcp

dd0cf05

sofstam added the WIP Work in progress label Jun 27, 2023

sofstam changed the title ~~Start adding kmcp~~ Add kmcp classifier Jun 27, 2023

sofstam and others added 16 commits June 27, 2023 13:47

Add kmcp code to local/profiling

f28c7a0

Add kmcp to subworkflows and start adding to nextflow_schema

1041c2c

Fix left-padding spaces

8fc3cb1

Add citation and usage.md

85aeac9

Add test configs for kmcp

55930a7

Prettier

3096e36

Fix typo

20e2c0b

Fix formatting

18fd6bb

Prettier

7d5bb19

Remove kmcp from standardisation profiles

3869bac

Merge branch 'dev' into add_kmcp_dev

4f4d2ee

Solve conflicts

6472f93

Adding kmcp_compute and kmcp_index

05c0b4c

Fix conflicts

720537f

Prettier

29d653b

Miss one bracket

da517c4

jfy133 and others added 8 commits July 25, 2023 11:49

Merge branch 'dev' into add_kmcp_dev

93239f9

Add index and search function

c80dda4

Add kmcp search

29ea089

Remove compute and index from include

7752f5e

Update kmcp modules

ea9019a

Remove parameters

e5d09fa

Add citation

e1e6dd8

Update usage.md

5d1d475

sofstam marked this pull request as ready for review August 1, 2023 11:46

sofstam and others added 9 commits August 15, 2023 15:36

Update docs/output.md

dee5c2d

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/output.md

dc0c2c7

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/usage.md

e64fd22

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/usage.md

1818534

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/usage/tutorials.md

91e65ff

Co-authored-by: James A. Fellows Yates <[email protected]>

Update README.md

3feda05

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/usage/tutorials.md

31f9b11

Co-authored-by: James A. Fellows Yates <[email protected]>

Update nextflow_schema.json

2506650

Co-authored-by: James A. Fellows Yates <[email protected]>

Update the help text of profiling mode

85ec872

sofstam added 7 commits August 16, 2023 17:13

Add help text for kmcp_save_search

95f7b11

Improve docs for kmcp

2547623

Add kmcp to tube

a476d70

Merge branch 'dev' into add_kmcp_dev

8aa5731

Add semicolon

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Add comment

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Split based on semicolon

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jfy133 requested changes Aug 18, 2023

View reviewed changes

jfy133 and others added 9 commits August 18, 2023 19:30

Apply suggestions from code review

7bc303d

Add missing commands from custom database build

502a92a

Add KMCP example similar to bracken

902fd19

Fix typo

482c14b

Update docs/usage.md

428881d

Co-authored-by: James A. Fellows Yates <[email protected]>

Docs formatting consistency

6394925

More minor formatting corrections

09b401d

Improve KMCp/Bracken db_params docs.

9af00c1

Improve error message

e5df2f9

jfy133 self-requested a review August 19, 2023 09:22

jfy133 approved these changes Aug 19, 2023

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jfy133 merged commit 697647f into nf-core:dev Aug 19, 2023
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Add kmcp classifier #312

Add kmcp classifier #312

sofstam commented Jun 27, 2023

github-actions bot commented Jun 27, 2023 •

edited

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sofstam commented Jul 20, 2023

jfy133 commented Aug 15, 2023 •

edited by sofstam

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Add kmcp classifier #312

Add kmcp classifier #312

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sofstam commented Jun 27, 2023

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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sofstam commented Jul 20, 2023

jfy133 commented Aug 15, 2023 • edited by sofstam Loading

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github-actions bot commented Jun 27, 2023 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️

jfy133 commented Aug 15, 2023 •

edited by sofstam

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