Json schema improvements by agusinac · Pull Request #777 · nf-core/mag

agusinac · 2025-03-24T14:36:15Z

This PR updates the JSON schema to be more complete

3.3.1 release

nvnieuwk · 2025-03-24T14:43:54Z

                "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$"
+                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "errorMessage": "short_reads_1 needs to be a file path with no spaces!"


can you also mention that the file needs to exist? (And also do this for each other file error message?)

Ah yes I will do that!

nvnieuwk · 2025-03-24T14:44:28Z

                    "type": "boolean",
                    "description": "Specifies that the input is single-end reads.",
                    "fa_icon": "fas fa-align-center",
+                    "default": false,


The default false option isn't necessary for booleans as we assume a boolean to be false by default

nvnieuwk · 2025-03-24T14:48:24Z

                },
                "bowtie2_mode": {
-                    "type": "string",
+                    "type": ["string", "boolean"],


Why a boolean here?

Because when I tested it with "--very-sensitive" it returns a json file in the result with bowtie2_mode: true so it seems that the flag returns a boolean ?

nvnieuwk

Great work!!!! Here are some comments :)

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

agusinac · 2025-03-24T15:28:31Z

I have encountered an unexpected behaviour when executing the following command:
nextflow run main.nf -profile test, docker --outdir results -stub --bowtie2_mode "--very-sensitive".

The above results in the following warning:
* --verySensitive: true

This results in the json receiving a boolean instead of a string. The nextflow_schema.json, line 743 has been changed to account for the boolean. After discussing with @nvnieuwk we thought this should be brought to your attention @jfy133

"bowtie2_mode": {
    "type": ["string", "boolean"],
    "description": "Bowtie2 alignment mode",
    "help_text": "Bowtie2 alignment mode options, for example: `--very-fast` , `--very-sensitive-local -N 1` , ... Must be used like this: --bowtie2_mode \"--very-sensitive\"",
    "pattern": "^\\'.*\\'$"
}

awgymer · 2025-03-24T23:01:11Z

I believe the only correct way to supply a param value which starts with -- is to use explicit equals:

 --bowtie2_mode="--very-sensitive"

jfy133 · 2025-03-25T18:36:08Z

Yeah I was personally never particularly happy with these flags, but it is what it is. Thanks for giving the solution @awgymer ! @agusinac could you check with Arthur's solution?

jfy133 · 2025-03-25T18:36:12Z

@nf-core-bot fix linting

agusinac · 2025-03-26T13:24:51Z

Yeah I was personally never particularly happy with these flags, but it is what it is. Thanks for giving the solution @awgymer ! @agusinac could you check with Arthur's solution?

I checked with Arthur's solution and adapted the nextflow_schema.json. The json file now returns a string, the help_text displays the correct way to call the flag as --bowtie2_mode="--very-sensitive" and json keyword pattern is updated to check the validation of the passed string.

jfy133 · 2025-03-26T18:21:54Z

                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
-                    "hidden": true
+                    "hidden": true,
+                    "help_text": "Location of pipeline test dataset files"


Everything in this file above this comment are all from the template, have you updated it there too @agusinac (or more likely @nvnieuwk )

Yes, I went through the whole document and added keywords if they were missing.

jfy133 · 2025-03-26T18:24:06Z

                "adapterremoval_adapter1": {
                    "type": "string",
                    "default": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG",
+                    "pattern": "^[ATGCRYKMSWBDHVN]*$",


I have a feeling this would only accept AGCTN, but I can't really tell from the documentation... so we will stick with this for now

It should accept any of the mentioned characters to be present either zero or more times. The adapter2 didn't contain any N and passed the test. I am happy to hear if this should be improved in the future!

jfy133 · 2025-03-26T18:25:45Z

Thanks @agusinac !

jfy133 and others added 4 commits February 13, 2025 14:06

Merge pull request nf-core#764 from nf-core/dev

b2377f1

3.3.1 release

Merge branch 'nf-core:master' into json-schema-improvements

222fe71

reviewed and added additional JSON keywords for improved validation

831d04b

Update CHANGELOG.md

e1f4e58

nvnieuwk reviewed Mar 24, 2025

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Comment thread nextflow_schema.json Outdated

nvnieuwk reviewed Mar 24, 2025

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Comment thread nextflow_schema.json Outdated

nvnieuwk reviewed Mar 24, 2025

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nvnieuwk requested changes Mar 24, 2025

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agusinac and others added 3 commits March 24, 2025 15:54

Update nextflow_schema.json

c1516d6

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Update nextflow_schema.json

98c519a

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

adjusted files based on @nvnieuwk comments

362ce33

jen-reeve linked an issue Mar 25, 2025 that may be closed by this pull request

JSON schema: Mag #778

Closed

15 tasks

nf-core-bot and others added 2 commits March 25, 2025 18:52

[automated] Fix code linting

dbff25c

Update nextflow_schema.json with tip of @awgymer

0d72e46

jfy133 approved these changes Mar 26, 2025

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Update CHANGELOG.md

85fe16b

jfy133 merged commit 5e57b2e into nf-core:dev Mar 26, 2025
5 of 15 checks passed

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