Automatic retrieval of input id.csv from test-datasets for test profile

[pmoris]

Description of feature

I'd like to change the test.config profile so that it points to an ids.csv file hosted in the test-datasets repository, instead of requiring the user to first manually create one.

I realize that the documentation explains that you need to create an ids.csv file yourself, but when I first tried the pipeline, I just tried adding -profile test,apptainer and expected it to work (like it does for the other pipelines I've used, e.g., https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/conf/test.config#L24). Instead I was greeted by the following error:

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input: the file or directory '${projectDir}/tests/sra_ids_test.csv' does not exist.

 -- Check script '/home/pmoris/.nextflow/assets/nf-core/fetchngs/./subworkflows/local/nf_core_fetchngs_utils/../../nf-core/nfvalidation_plugin_utils/main.nf' at line: 55 or see '.nextflow.log' file for more details

and was left trying to figure if something was wrong on my end, with the latest release or if the test profile simply didn't work the way I was expecting.

I'm happy to fix this myself, but wanted to first check if you'd rather have me:

1. create a new test file with the same contents as the one in the main README (https://github.com/nf-core/fetchngs/tree/1.11.0?tab=readme-ov-file#usage),
2. re-use one of the existing files in the test-datasets repo that are being used for unit testing (e.g., https://github.com/nf-core/test-datasets/blob/fetchngs/sra_ids_test.csv),
   or
3. just remove the line pointing to the ${projectDir} input file in the test.config file, so that at the very least it throws a warning about the input not being provided, rather than that an input file couldn't be found in the expected location.

(Thanks for the amazing tool by the way, it's made fastq retrieval so much easier for me.)

[bug1303]

The csv file is actually part of the release, you can see it at https://github.com/nf-core/fetchngs/blob/1.11.0/tests/sra_ids_test.csv

and it does get fetched:

cat $NXF_HOME/assets/nf-core/fetchngs/tests/sra_ids_test.csv
ERR1160846
GSE214215
SRR12848126

When I launch the pipeline with test profile, it reports:

[...]
nf-core/fetchngs v1.11.0-g04ee503
[...]
projectDir : /xxxxxxx/nxf-home/assets/nf-core/fetchngs

So, projectDir is set to the expected path, but is not expanded properly.

This is on nextflow version 23.04.1.5866

[bug1303]

I realized it can be solved with a simple fix:
bug1303@798be6f
Then it actually finds the csv file.

However, version 1.12.0 of fetchngs is supposed to come out very soon, and there it is set to fetch input from test-datasets:
https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv

[maxulysse]

yeah, sorry about that, this issue has been fixed in dev, and we're preparing the release

[maxulysse]

it was a simple why did I use single quotes instead of double quotes error

[pmoris]

Oh, I see! Thanks for the info! Closing this issue then!