ERROR ~ Script compilation error cause: you tried to assign a value to the class 'java.lang.String'

Training
1

I was running Hello Nextflow training on my local computer. My setup was failing at param.input part. It took me a while to find the solution:

export NXF_SYNTAX_PARSER=v2

Would it be possible to add a text block to tell learners about this error and how to fix it?

2

Hi @b-brankovics , thanks for reporting this. The parser requirement is documented on the Getting Started page for the course as follows:

Version requirements

This training is designed for Nextflow 25.10.2 or later with the v2 syntax parser ENABLED. If you are using a local or custom environment, please make sure you are using the correct settings as documented here.

But I understand that might not stand out if you skimmed past those instructions. I’ll see if we can add a note for anyone who has the same problem.

3

Confirmed that this is the first time that the v1 syntax parser causes this error.

Here’s a PR to add an admonition in the right place:

5

Hi, just want to confirm, does the Seqera Containers repositories include all the docker image that we may need to write a nextflow script? i want to use a toolkit called sratools, but cannot find the relevant docker image in Seqera Containers :smiling_face_with_tear:

6

Hi @Rachel, Seqera Containers covers packages in pypi, bioconda and conda-forge. If you’re using tools that are not distributed through one of those channels, you may need to find a container elsewhere or build it yourself.

That being said, I see we have one for ‘sra-tools’ (with a hyphen): Containers | Seqera

Have a look and see if that’s what you’re looking for. Let me know if you need help finding another source of containers.

7

Hi @GeraldineVdA and @ewels, thanks for picking this up so fast. I definitely missed that section. I was looking for section that mentions local environment, the structuring and heading suggested to me that this part refers to the Codespaces.

The info block stated this “In older workflows, you may see that whole params block written as just input = 'Holà mundo!'.“ And the text above mentions the change with v 25.10.2 and later, but does not mention the syntax parser. That part could be a good location to also mention the difference of the different syntax parsers.

8

Thanks @b-brankovics for this feedback, I’ll take another look and see if we can make this clearer in the text.

9

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