So it seems my issue is actually < Mahesh Binzer Panchal> ex nf-core #rubber-duck

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So it seems my issue is actually <@UNMC49PJS> :exp...

# rubber-duck

Maxime Garcia

05/04/2026, 9:11 AM

So it seems my issue is actually @Mahesh Binzer-Panchal 🤯

Mahesh Binzer-Panchal

05/04/2026, 9:17 AM

Huh? What's happening?

Maxime Garcia

05/04/2026, 9:18 AM

I don't know, but somehow, the map I have for you which looks totally fine for me is failing the linting if not placed last

Mahesh Binzer-Panchal

05/04/2026, 9:19 AM

Which lint? nf-core or nextflow?

Maxime Garcia

05/04/2026, 9:19 AM

nf-core

Maxime Garcia

05/04/2026, 9:20 AM

and not failing, but erroring in a way that seems to indicate a parsing issue

Maxime Garcia

05/04/2026, 9:21 AM

Look what I had to do in the nextflow.config file in https://github.com/nf-core/seqinspector/pull/233/changes

Maxime Garcia

05/04/2026, 9:21 AM

I really though I am going crazy, but it works

Mahesh Binzer-Panchal

05/04/2026, 9:25 AM

Is it linting or the RO crate stuff?

Maxime Garcia

05/04/2026, 9:26 AM

so it's in linting, it's an error, but does not fail anything, it just cannot parse the contributors, and it should do something with RO crate

Maxime Garcia

05/04/2026, 9:27 AM

As I knew something was wrong with the contributors, I removed everyone, and added people back one by one

Maxime Garcia

05/04/2026, 9:29 AM

and that's how I noticed an issue

Louis Le Nézet

05/04/2026, 9:44 AM

Is there any strange invisible character ?

Mahesh Binzer-Panchal

05/04/2026, 9:46 AM

Then my entry would always error right?

Louis Le Nézet

05/04/2026, 9:48 AM

How did you obtain the error, I'm curious now 😄

Mahesh Binzer-Panchal

05/04/2026, 9:48 AM

The parsing function seems to be doing some replace stuff which I don't get

Copy code

# Use curly brackets for dictionaries
        contributors_str = contributors_str.replace("], [", "}, {").replace("[[", "[{").replace("]]", "}]")

🫠 1

Mahesh Binzer-Panchal

05/04/2026, 9:50 AM

It's updating a lot of stuff in the parse:

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# Read and parse manifest.contributors. Normalise and fix its fields,
    # and return as a list of dictionaries
    def parse_manifest_contributors(self) -> list:
        field_names = ["name", "affiliation", "github", "contribution", "orcid", "email"]
        # Grab the contributor list and convert to JSON
        # TODO: can be removed once we switch to `nextflow config -o json`
        contributors_str = self.pipeline_obj.nf_config["manifest.contributors"]
        log.debug(f"manifest.contributors: {contributors_str}")
        # JSON uses double quotes, not single quotes
        contributors_str = contributors_str.replace("'", '"')
        for key in field_names:
            # All dictionary keys need to be quoted
            contributors_str = contributors_str.replace(f"{key}:", f'"{key}":')
        # Use curly brackets for dictionaries
        contributors_str = contributors_str.replace("], [", "}, {").replace("[[", "[{").replace("]]", "}]")
        log.debug(f"manifest.contributors (normalised): {contributors_str}")
        try:
            contributors = json.loads(contributors_str)
        except json.JSONDecodeError as exc:
            log.error(
                "Could not parse `manifest.contributors` from nextflow.config. "
                "Expected a list of maps, for example: [[name: 'First Last', github: 'user']]. "
                f"Normalised string passed to JSON parser was: {contributors_str!r}. "
                f"JSON decoding error: {exc}"
            )
            return []

Mahesh Binzer-Panchal

05/04/2026, 9:50 AM

My guess is the issue is in there.

Mahesh Binzer-Panchal

05/04/2026, 9:55 AM

Maxime, can you run with the debug settings to see what the before looks like?

Copy code

log.debug(f"manifest.contributors: {contributors_str}")

Mahesh Binzer-Panchal

05/04/2026, 9:56 AM

There's probably not a

Copy code

log.debug(f"manifest.contributors (normalised): {contributors_str}")

for mine

Maxime Garcia

05/04/2026, 10:32 AM

Copy code

DEBUG    manifest.contributors: [[name:'Adrien Coulier', affiliation:'Pixelgen Technologies', github:'Aratz', contribution:['author'], orcid:'0000-0003-2702-1103'], [name:'Alfred Kedhammar', affiliation:'Clinical     rocrate.py:404
         Genomics', github:'kedhammar', contribution:['author']], [name:'Agrima Bhatt', affiliation:'National Genomics Infrastructure', github:'agrima2010', contribution:['author'], orcid:'0009-0004-5536-7210'],
         [name:'Maxime U Garcia', affiliation:'National Genomics Infrastructure', github:'maxulysse', contribution:['contributor', 'maintainer'], orcid:'0000-0003-2827-9261'], [name:'Natalia Garcia Garcia',
         github:'nggvs', contribution:['contributor']], [name:'Franziska Bonath', affiliation:'National Genomics Infrastructure', github:'FranBonath', contribution:['author'], orcid:'0000-0002-1270-1504'],
         [name:'Pontus Höjer', affiliation:'National Genomics Infrastructure', github:'pontushojer', contribution:['contributor'], orcid:'0000-0001-8010-4755'], [name:'Edmund Miller', affiliation:'Seqera',
         github:'edmundmiller', contribution:['contributor']], [name:'Ramprasad Neethiraj', affiliation:'Clinical Genomics', github:'ramprasadn', contribution:['author'], orcid:'0000-0001-7313-3734'], [name:'Matilda
         Åslin', affiliation:'National Genomics Infrastructure', github:'matrulda', contribution:['author'], orcid:'0000-0002-2450-6415'], [name:'Patricie Skaláková', affiliation:'Masaryk University',
         github:'Patricie34', contribution:['contributor'], orcid:'0009-0009-0647-7639'], [name:'Eliott Bosshard', affiliation:'Clinical Genomics', github:'EliottBo', contribution:['contributor'],
         orcid:'0009-0000-2384-0369'], [name:'Karthik Nair', affiliation:'National Genomics Infrastructure', github:'KarNair', contribution:['contributor']], [name:'Matthias Zepper', affiliation:'National Genomics
         Infrastructure', github:'MatthiasZepper', contribution:['author'], orcid:'0000-0003-2880-8581'], [name:'Nelly Nyawira Nkonge', affiliation:'National Genomics Infrastructure', github:'nkongenelly',
         contribution:['contributor'], orcid:'0000-0002-0396-8573'], [name:'Beatriz Vinhas', affiliation:'Clinical Genomics', github:'beatrizsavinhas', contribution:['contributor']], [name:'Júlia Mir Pedrol',
         affiliation:'Center For Genomics Regulation', github:'mirpedrol', contribution:['contributor'], orcid:'0000-0001-6104-9260'], [name:'Cristina Tuñí i Domínguez', affiliation:'Flowmics', github:'ctuni',
         contribution:['contributor']], [name:'Johannes Alneberg', affiliation:'National Genomics Infrastructure', github:'alneberg', contribution:['contributor'], orcid:'0000-0002-2467-008X'], [name:'Annick
         Renevey', affiliation:'Clinical Genomics', github:'rannick', contribution:['contributor'], orcid:'0000-0001-7411-6063'], [name:'Adam Talbot', affiliation:'Seqera', github:'adamrtalbot',
         contribution:['contributor']], [name:'Jonas Kjellin', affiliation:'National Genomics Infrastructure', github:'kjellinjonas', contribution:['contributor'], orcid:'0000-0002-3830-7046'], [name:'Mahesh
         Binzer-Panchal', affiliation:'National Bioinformatics Infrastructure Sweden', github:'mahesh-panchal', contribution:['contributor'], orcid:'0000-0003-1675-0677'], [name:'Tori Griffin', affiliation:'National
         Genomics Infrastructure', github:'torigiffin', contribution:['contributor']]]
DEBUG    manifest.contributors (normalised): [{"name":"Adrien Coulier", "affiliation":"Pixelgen Technologies", "github":"Aratz", "contribution":["author"], "orcid":"0000-0003-2702-1103"}, {"name":"Alfred Kedhammar",  rocrate.py:412
         "affiliation":"Clinical Genomics", "github":"kedhammar", "contribution":["author"]}, {"name":"Agrima Bhatt", "affiliation":"National Genomics Infrastructure", "github":"agrima2010",
         "contribution":["author"], "orcid":"0009-0004-5536-7210"}, {"name":"Maxime U Garcia", "affiliation":"National Genomics Infrastructure", "github":"maxulysse", "contribution":["contributor", "maintainer"],
         "orcid":"0000-0003-2827-9261"}, {"name":"Natalia Garcia Garcia", "github":"nggvs", "contribution":["contributor"]}, {"name":"Franziska Bonath", "affiliation":"National Genomics Infrastructure",
         "github":"FranBonath", "contribution":["author"], "orcid":"0000-0002-1270-1504"}, {"name":"Pontus Höjer", "affiliation":"National Genomics Infrastructure", "github":"pontushojer",
         "contribution":["contributor"], "orcid":"0000-0001-8010-4755"}, {"name":"Edmund Miller", "affiliation":"Seqera", "github":"edmundmiller", "contribution":["contributor"]}, {"name":"Ramprasad Neethiraj",
         "affiliation":"Clinical Genomics", "github":"ramprasadn", "contribution":["author"], "orcid":"0000-0001-7313-3734"}, {"name":"Matilda Åslin", "affiliation":"National Genomics Infrastructure",
         "github":"matrulda", "contribution":["author"], "orcid":"0000-0002-2450-6415"}, {"name":"Patricie Skaláková", "affiliation":"Masaryk University", "github":"Patricie34", "contribution":["contributor"],
         "orcid":"0009-0009-0647-7639"}, {"name":"Eliott Bosshard", "affiliation":"Clinical Genomics", "github":"EliottBo", "contribution":["contributor"], "orcid":"0009-0000-2384-0369"}, {"name":"Karthik Nair",
         "affiliation":"National Genomics Infrastructure", "github":"KarNair", "contribution":["contributor"]}, {"name":"Matthias Zepper", "affiliation":"National Genomics Infrastructure", "github":"MatthiasZepper",
         "contribution":["author"], "orcid":"0000-0003-2880-8581"}, {"name":"Nelly Nyawira Nkonge", "affiliation":"National Genomics Infrastructure", "github":"nkongenelly", "contribution":["contributor"],
         "orcid":"0000-0002-0396-8573"}, {"name":"Beatriz Vinhas", "affiliation":"Clinical Genomics", "github":"beatrizsavinhas", "contribution":["contributor"]}, {"name":"Júlia Mir Pedrol", "affiliation":"Center For
         Genomics Regulation", "github":"mirpedrol", "contribution":["contributor"], "orcid":"0000-0001-6104-9260"}, {"name":"Cristina Tuñí i Domínguez", "affiliation":"Flowmics", "github":"ctuni",
         "contribution":["contributor"]}, {"name":"Johannes Alneberg", "affiliation":"National Genomics Infrastructure", "github":"alneberg", "contribution":["contributor"], "orcid":"0000-0002-2467-008X"},
         {"name":"Annick Renevey", "affiliation":"Clinical Genomics", "github":"rannick", "contribution":["contributor"], "orcid":"0000-0001-7411-6063"}, {"name":"Adam Talbot", "affiliation":"Seqera",
         "github":"adamrtalbot", "contribution":["contributor"]}, {"name":"Jonas Kjellin", "affiliation":"National Genomics Infrastructure", "github":"kjellinjonas", "contribution":["contributor"],
         "orcid":"0000-0002-3830-7046"}, {"name":"Mahesh Binzer-Panchal", "affiliation":"National Bioinformatics Infrastructure Sweden", "github":"mahesh-panchal", "contribution":["contributor"],
         "orcid":"0000-0003-1675-0677"}, {"name":"Tori Griffin", "affiliation":"National Genomics Infrastructure", "github":"torigiffin", "contribution":["contributor"}]]
ERROR    Could not parse `manifest.contributors` from nextflow.config. Expected a list of maps, for example: []. Normalised string passed to JSON parser was: '[{"name":"Adrien Coulier", "affiliation":"Pixelgen        rocrate.py:416
         Technologies", "github":"Aratz", "contribution":["author"], "orcid":"0000-0003-2702-1103"}, {"name":"Alfred Kedhammar", "affiliation":"Clinical Genomics", "github":"kedhammar", "contribution":["author"]},
         {"name":"Agrima Bhatt", "affiliation":"National Genomics Infrastructure", "github":"agrima2010", "contribution":["author"], "orcid":"0009-0004-5536-7210"}, {"name":"Maxime U Garcia", "affiliation":"National
         Genomics Infrastructure", "github":"maxulysse", "contribution":["contributor", "maintainer"], "orcid":"0000-0003-2827-9261"}, {"name":"Natalia Garcia Garcia", "github":"nggvs",
         "contribution":["contributor"]}, {"name":"Franziska Bonath", "affiliation":"National Genomics Infrastructure", "github":"FranBonath", "contribution":["author"], "orcid":"0000-0002-1270-1504"},
         {"name":"Pontus Höjer", "affiliation":"National Genomics Infrastructure", "github":"pontushojer", "contribution":["contributor"], "orcid":"0000-0001-8010-4755"}, {"name":"Edmund Miller",
         "affiliation":"Seqera", "github":"edmundmiller", "contribution":["contributor"]}, {"name":"Ramprasad Neethiraj", "affiliation":"Clinical Genomics", "github":"ramprasadn", "contribution":["author"],
         "orcid":"0000-0001-7313-3734"}, {"name":"Matilda Åslin", "affiliation":"National Genomics Infrastructure", "github":"matrulda", "contribution":["author"], "orcid":"0000-0002-2450-6415"}, {"name":"Patricie
         Skaláková", "affiliation":"Masaryk University", "github":"Patricie34", "contribution":["contributor"], "orcid":"0009-0009-0647-7639"}, {"name":"Eliott Bosshard", "affiliation":"Clinical Genomics",
         "github":"EliottBo", "contribution":["contributor"], "orcid":"0009-0000-2384-0369"}, {"name":"Karthik Nair", "affiliation":"National Genomics Infrastructure", "github":"KarNair",
         "contribution":["contributor"]}, {"name":"Matthias Zepper", "affiliation":"National Genomics Infrastructure", "github":"MatthiasZepper", "contribution":["author"], "orcid":"0000-0003-2880-8581"},
         {"name":"Nelly Nyawira Nkonge", "affiliation":"National Genomics Infrastructure", "github":"nkongenelly", "contribution":["contributor"], "orcid":"0000-0002-0396-8573"}, {"name":"Beatriz Vinhas",
         "affiliation":"Clinical Genomics", "github":"beatrizsavinhas", "contribution":["contributor"]}, {"name":"Júlia Mir Pedrol", "affiliation":"Center For Genomics Regulation", "github":"mirpedrol",
         "contribution":["contributor"], "orcid":"0000-0001-6104-9260"}, {"name":"Cristina Tuñí i Domínguez", "affiliation":"Flowmics", "github":"ctuni", "contribution":["contributor"]}, {"name":"Johannes Alneberg",
         "affiliation":"National Genomics Infrastructure", "github":"alneberg", "contribution":["contributor"], "orcid":"0000-0002-2467-008X"}, {"name":"Annick Renevey", "affiliation":"Clinical Genomics",
         "github":"rannick", "contribution":["contributor"], "orcid":"0000-0001-7411-6063"}, {"name":"Adam Talbot", "affiliation":"Seqera", "github":"adamrtalbot", "contribution":["contributor"]}, {"name":"Jonas
         Kjellin", "affiliation":"National Genomics Infrastructure", "github":"kjellinjonas", "contribution":["contributor"], "orcid":"0000-0002-3830-7046"}, {"name":"Mahesh Binzer-Panchal", "affiliation":"National
         Bioinformatics Infrastructure Sweden", "github":"mahesh-panchal", "contribution":["contributor"], "orcid":"0000-0003-1675-0677"}, {"name":"Tori Griffin", "affiliation":"National Genomics Infrastructure",
         "github":"torigiffin", "contribution":["contributor"}]]'. JSON decoding error: Expecting ',' delimiter: line 1 column 3454 (char 3453)
ERROR    No authors found in pipeline manifest. Proceeding without adding authors to the RO-Crate.                                                                                                                       rocrate.py:281

Maxime Garcia

05/04/2026, 10:32 AM

nope, you are there

Maxime Garcia

05/04/2026, 10:33 AM

And when I put you back in last, issue is no longer there

Maxime Garcia

05/04/2026, 10:33 AM

Untitled

Mahesh Binzer-Panchal

05/04/2026, 10:59 AM

There's two outputs. One is unnormalized and the other is normalized. I'm not expecting my name in the normalized output. Also why is Annick's name there twice? She and my name both appear to have carriage returns following the first name.

👀 1

Mahesh Binzer-Panchal

05/04/2026, 11:00 AM

Or is that your own formatting?

Maxime Garcia

05/04/2026, 11:03 AM

I copy pasted from the terminal, so formatting is definitively borked

Maxime Garcia

05/04/2026, 11:03 AM

but you are in both unnormalized and normalized

Maxime Garcia

05/04/2026, 11:03 AM

I haven't noticed any duplicates in name

Mahesh Binzer-Panchal

05/04/2026, 12:07 PM

Does Tori griffin have an error in her entry?

Copy code

"torigiffin", "contribution":["contributor"}]]
                                           ^

Maxime Garcia

05/04/2026, 12:13 PM

nope

Maxime Garcia

05/04/2026, 12:13 PM

That only comes when you're put in not in last

Mahesh Binzer-Panchal

05/04/2026, 12:18 PM

Oh, my mistake. That was from the normalised list. But wait. Are you sure it's me, or the fact that Tori doesn't have an orcid?

Maxime Garcia

05/04/2026, 12:24 PM

iep

Maxime Garcia

05/04/2026, 12:24 PM

pretty sure it's you, given your place in the list

Maxime Garcia

05/04/2026, 12:25 PM

you you've given me more ideas

Maxime Garcia

05/04/2026, 12:25 PM

and @mashehu too

Maxime Garcia

05/04/2026, 12:25 PM

So I'll keep investigating

Mahesh Binzer-Panchal

05/04/2026, 12:26 PM

I think the fix might be

Copy code

# Replace only the outermost brackets (not nested ones)
if contributors_str.startswith("[["):
    contributors_str = "[{" + contributors_str[2:]
if contributors_str.endswith("]]"):
    contributors_str = contributors_str[:-2] + "}]"
contributors_str = contributors_str.replace("], [", "}, {")

mashehu

05/04/2026, 12:34 PM

the fix will most probably be https://github.com/nf-core/tools/issues/4204

Mahesh Binzer-Panchal

05/04/2026, 12:36 PM

As in you're going to do the switch to

nextflow config -o json

as the solution to this?

mashehu

05/04/2026, 12:37 PM

yep, to avoid all the awkward json normalization

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