Fix fasta input - Githubissues

jtangrot commented 1 year ago

This PR addresses #542. A module was added to change tabs to spaces in description part of sequence names when using fasta input. The descriptions are kept as part of the sequence name. Removing the tabs will remove the problem with the sequence on a line of its own.

PR checklist

[x] 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/ampliseq branch on the nf-core/test-datasets repository.
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jtangrot commented 1 year ago

I have added descriptions to some of the file names in the fasta file used for testing. I don't know what else needs changing in the testing?

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 83aca46

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Parameter `input` is not defined in the correct subschema (input_output_options) ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config` ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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erikrikarddaniel commented 1 year ago

I have added descriptions to some of the file names in the fasta file used for testing. I don't know what else needs changing in the testing?

Perfect.

erikrikarddaniel commented 1 year ago

There are tests failing, so I'm waiting with my review. Need to go on an errand now.

d4straub commented 1 year ago

There is a reproducible (here in github) error with -profile test,docker. The error message is

No such variable: info

 -- Check script './workflows/../subworkflows/local/parse_input.nf' at line: 63 or see '.nextflow.log' file for more details
Argument of 'channel.from' method cannot be a channel object — Likely you can replace the use of 'channel.from' with the channel object itself

 -- Check script './workflows/ampliseq.nf' at line: 652 or see '.nextflow.log' file for more details

I do not understand whats happening though.

erikrikarddaniel commented 1 year ago

There is a reproducible (here in github) error with -profile test,docker. The error message is

No such variable: info

 -- Check script './workflows/../subworkflows/local/parse_input.nf' at line: 63 or see '.nextflow.log' file for more details
Argument of 'channel.from' method cannot be a channel object — Likely you can replace the use of 'channel.from' with the channel object itself

 -- Check script './workflows/ampliseq.nf' at line: 652 or see '.nextflow.log' file for more details

I do not understand whats happening though.

The error message is clear enough -- and Channel.from(ch_multiqc_config) looks like it could be the offender, since it's calling the method with a channel (possibly empty) -- but strange that it only affects docker and shows up in a file that's not touched. It's input can have been touched of course, but still strange that singularity works -- or does it (I don't really understand this test)?

d4straub commented 1 year ago

Well, that works for me flawless:

nextflow pull jtangrot/ampliseq
nextflow pull jtangrot/ampliseq -r fix_fasta_input
nextflow run jtangrot/ampliseq -r fix_fasta_input -profile test,singularity --outdir results_jtangrot-fix_fasta_input__test
nextflow run jtangrot/ampliseq -r fix_fasta_input -profile test,docker --outdir results_jtangrot-fix_fasta_input__test_docker

jtangrot commented 1 year ago

Thanks for looking into this. I really have no clue how to fix this...

d4straub commented 1 year ago

Maybe bother the github actions experts in the nf-core slack?

d4straub commented 1 year ago

The failing test nf-core CI / Run pipeline with test data (latest-everything) (pull_request) uses N E X T F L O W ~ version 23.02.0-edge, which was released 3 days ago. I strongly suspect that the nextflow version causes that issue. If that is true, then we can ignore the failing test for that PR. I can check that on Monday.

erikrikarddaniel commented 1 year ago

Or maybe fix the problem so it works with the new version? Sooner or later we might have to anyway.

erikrikarddaniel commented 1 year ago

Did the test get stuck? I think this looks fine with the change to the channel, but wanted to wait until the test completed.

d4straub commented 1 year ago

NXF_VER=23.02.0-edge nextflow run nf-core/ampliseq -r 2.4.1 -profile test,singularity leads to the same error, therefore confirmed that its the nextflow version, not this PR.

Or maybe fix the problem so it works with the new version? Sooner or later we might have to anyway.

Thats an idea, but because it seems to have nothing to do with this PR, I was rather leaning towards fixing this separately. Anyway, the latest commit up there is only addressing the problem partially I think. It seems we deviate from the nf-core template 2.7.2, i.e. the whole line might have to be removed? I guess that was my mistake when doing the template update.

erikrikarddaniel commented 1 year ago

I'm fine with either approving this latest commit or making a fuller attempt at addressing issues from an upgrade of Nextflow.

jtangrot commented 1 year ago

Thanks!

nf-core / ampliseq

Fix fasta input #544

PR checklist

`nf-core lint` overall result: Passed :white_check_mark: :warning:

nf-core / ampliseq

Fix fasta input #544

PR checklist

nf-core lint overall result: Passed :white_check_mark: :warning:

`nf-core lint` overall result: Passed :white_check_mark: :warning: