Make release 1.0.0

[delfiterradas]

Closes #80:

Added

• [#87] - Add local test profile (@delfiterradas, review by @atrigila).
• [#79] - Add exit status for RCLONE modules in multiqc report (@delfiterradas, review by @atrigila).
• [#74] - Implement warning and --download parameter when working with remote directories and SHA checksums (@delfiterradas, review by @atrigila, @apeltzer and @antoniasaracco).
• [#67] - Copy only files which are successfully validated (@delfiterradas, review by @atrigila and @antoniasaracco).
• [#57] - Add nf-tests with edge cases(@atrigila, review by @delfiterradas).
• [#55] - Add subdirectories with sample id to results. Improvements to MultiQC report (width of columns, sections and sub-section headers)colors to multiqc results and display first errors in tables (@atrigila, review by @delfiterradas).
• [#54] - Add colors to multiqc results and display first errors in tables (@atrigila, review by @delfiterradas).
• [#31] - Compute checksum for each input file (@delfiterradas, review by @atrigila).
• [#35] - Compare generated checksum to given checksum in input and update test profiles (@delfiterradas, review by @atrigila).
• [#46] - Import Rclone module from nf-core(@antoniasaracco, review by @delfiterradas).
• [#41] - Generate MultiQC Report with comparechecksum tables and input samplesheet (@delfiterradas, review by @atrigila).
• [#49] - Install RCLONE_CHECK and RCLONE_CHECKSUM modules from nf-core (@delfiterradas, review by @atrigila and @antoniasaracco).
• [#59] - Create pipeline documentation (@antoniasaracco, review by @atrigila and @delfiterradas).

Fixed

• [#84] - Update RCLONE_ modules, enhance source and destination path handling, add local create_filter_list module and other small fixes (@delfiterradas, review by @atrigila).
• [#83] - Add apptainer version to avoid error in CI test (@delfiterradas, review by @atrigila).
• [#78] - Fixed linting issues reported by nf-core and Nextflow, and updated rclone modules and nf-tests to sort generated report files for deterministic snapshots (@atrigila, review by @delfiterradas and @antoniasaracco).
• [#76] - Remove --one-way from rclone/checksum confi (@delfiterradas, review by @atrigila and @antoniasaracco).
• [#73] - Create tmp files_to_copy.tx avoiding error with write permissions in work directory (@delfiterradas, review by @atrigila and @antoniasaracco).

[delfiterradas]

Hi @mazzalab and @ewels,
Thanks so much for taking the time to review the PR and for all the helpful suggestions! I’ve gone through all the comments and implemented the requested changes. Whenever you have a chance, it would be great if you could have another look at the updated version and let me know what you think :)

[LouisLeNezet]

Hi,

You will found a few comments below, but I don't see any issue.

On a more general aspect, would it be possible to also use file level informations in the input samplesheet.
Would something like the following be possible:

sample,input,output_path,checksum_md5
sample,ftp://url/my_file.txt,output_path/data,0e646ea1c354aed1654

[delfiterradas]

Hi @LouisLeNezet, thank you so much for taking the time to review the pipeline and for your suggestions!
I will start working on the changes in #93 and can let you know when it is done

[delfiterradas]

Hi @LouisLeNezet, we have addressed your suggestions and implemented the necessary changes.

When you have the time would you mind taking a look at the code again and letting us know what you think? ☺️

Also, regarding your question:

On a more general aspect, would it be possible to also use file level informations in the input samplesheet. Would something like the following be possible:

sample,input,output_path,checksum_md5
sample,ftp://url/my_file.txt,output_path/data,0e646ea1c354aed1654

This is not currently supported. For now, we intentionally kept the checksum input format aligned with the checksum file expected by rclone checksum, which simplifies both parsing and validation. We could consider supporting file level checksums directly in the samplesheet in a future iteration.

---

Please let me know if there is anything I missed.
Thank you!

[LouisLeNezet]

I don't see anything blocking code wise.
Just a little comment bellow on unittest coverage.
The code is clean and well documented, you might just need at some point to think about a logo 😉

[LouisLeNezet]

For this subworkflow, it could be nice to have a dedicated nf-test, so that you could easily test the different input / warning / error conditions.
You can also test only a function like function "validateInputParameters" in a function.nf.test.
This way you can test each condition without running the whole pipeline.

This can be an issue for now, if you want to release.

[delfiterradas]

Yes, this makes sense. I will go ahead and open an issue to include this afterwards :)

[mazzalab]

I don't see problems. It looks like a good review

[delfiterradas]

Thank you all for your time and suggestions!