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Update simpleaf to 0.17.2 #6319
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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 Thanks, |
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 |
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). |
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 Best, |
If you ask on the nf-core slack you can get added to the organisation and they'll run for you |
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 theindex
directory generated bysimpleaf 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.versions.yml
file.label
nf-core modules test <MODULE> --profile docker
nf-core modules test <MODULE> --profile singularity
nf-core modules test <MODULE> --profile conda
nf-core subworkflows test <SUBWORKFLOW> --profile docker
nf-core subworkflows test <SUBWORKFLOW> --profile singularity
nf-core subworkflows test <SUBWORKFLOW> --profile conda