Upgrade simpleaf modules to 0.17.2

[DongzeHE]

PR checklist

See discussion at here. This pull request is still working in progress.

In brief, I am updating simpleaf in scrnaseq and end up being here updating the central module. first. Except udpating the conda and docker image versions of simpleaf, I added an input item val no_piscem because by default, the latest simpleaf uses piscem, instead salmon, for indexing and mapping, this entirely changes the layout of the index directory generated by simpleaf index. I think the changes I have made will work fine as I tested when creating the other PR. However, I do not know how to update the MD5sums in the "snapshot" files.

• This comment contains a description of changes (with reason).
• [] If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[SPPearce]

Run nf-core modules test simpleaf --update to update the snapshots

[an-altosian]

Hi all, after a discussion with @rob-p, I think it might be worthy to expose all parameters supported by simpleaf index and simpleaf quant and make the processes more flexible, mainly because this module will be used across nf-core. I have came up with a design, as shown in the meta.yml file under simpleaf/index folder and simpleaf/quant folder. could anyone review to see if the input and output make sense, or we would like to hide some of the parameters?

Thanks,
Dongze

[SPPearce]

The guidelines are that files and mandatory non-file parameters should be given as input channels, other non-mandatory parameters should be passed through the use of ext.args. These non mandatory parameters can then be adjusted by the pipeline and/or the end-user by the use of config files.

[SPPearce]

We don't want to try to replicate the tool documentation of all the parameters, or expose them all individually (some tools have many possible options).

[an-altosian]

I think I am done with the implmenetation. Thanks to the information and guidance you provided, I basically only updated the version of simpleaf and wrote a function for processing the permitlist generation options, because it must be inferred from the ext.args and the whitelist input channel at the same time.

The commit has passed nf-core modules test simpleaf locally. Let's see if it can make github workflow actions happy.

Best,
Dongze

[SPPearce]

If you ask on the nf-core slack you can get added to the organisation and they'll run for you