Possible bug in logic code related to mature, hairpin and species setup

[lpantano]

Description of the bug

For this PR I realized that I can see there are a few things that will generate problems due to the duality between

• params.mirtrace_species
• params.mirna_gtf
• params.mature
• params.hairpin
• params.mirgenedb_*

params.mirtrace_species is used for miRTrace.
params.mirtrace_species is re-used for mirtop_quant when params.mature and params.hairpin and params.mirna_gtf are set up

all the params.mirgendb_* is used for mirtop_quant when they are set.

So the logic should be:

you set up params.mirgendb_* or params.mirna_gtf, params.mature, params.hairpin, not both.

you set up params.mirtrace_species if you want to use miRTrace or default miRBase files(params.mirna_gtf, params.mature, params.hairpin)

if user set up params.mirgendb_* and wants to run miRTrace, then params.mirtrace_species is used with miRTrace and params.mirgendb_species is used with miRTop. I don't think this is happening right.

Maybe we need a meeting to sort this out?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[nschcolnicov]

I think this should be fixed simply by updating the line mentioned by Lorena:

smrnaseq/subworkflows/local/prepare_genome/main.nf

Line 37 in 874ef64

ch_mirna_gtf = val_mirna_gtf ? Channel.empty() : ( mirna_gtf_from_species ? Channel.fromPath(mirna_gtf_from_species, checkIfExists: true).collect() : Channel.empty() ) //TODO for ch_mirna_gtf, shouldn't it try to build a channel.fromPath with params.mirna_gtf, if true? (instead of setting it to empty). Is this parameter used for non mirgenedb runs?

with something like this:

ch_mirna_gtf              = val_mirna_gtf                 ?  Channel.fromPath(val_mirna_gtf, checkIfExists: true).collect() : ( mirna_gtf_from_species ? Channel.fromPath(mirna_gtf_from_species, checkIfExists: true).collect() :  Channel.empty() )

But we probably would need to update the CI tests as well, and check if there is any other issue that arises from this change

[lpantano]

I think this issue is a little bit bigger scope. This is about how the pipeline setup the variables whether people want to use miRBase files or mirgeneDB, and together with miRTrace. I didn't test it but , I don't think will work well. When I run test_mirgendb config file, mirtop doesn't run, because mirtrace_species is not setup. But it should run, actually mirtrace should be able to run as well, even if people use mirgendb files to quantify.

[atrigila]

The issue was solved in #386 but some improvements in design can be made regarding the use of these databases in the future.
Some ideas discussed are:

• Use a single channel with hairpin, mature, gtf and species. This channel can have an associated metamap adding the origin DB (mirgeneDB or other) for tracking.
• There could be some checks that ensure that the 3 files come from the same database.
• The checks will also ensure that one single channel is populated and used across the whole pipeline. We could avoid having several params/channels referring to similar information. This is similar to what is done will the protocols.
• The species can likely be "translated" from other databases to mirTrace nomenclature by removing/adding a capital letter at the beginning (e.g. "hsa" to "Hsa").
• The gtf from each species could obtained automatically from these DBs using getGenomeAttribute() as we do with iGenomes.

[nschcolnicov]

Closing this ticket, as the issue described was solved in #386. @lpantano Feel free to open a new one, if you think there was something else to work on