Adding TRUST4 module

[Joaodemeirelles]

Draft for the TRUST4 module addition.

Since TRUST4 can be execute with single-end reads, paired-end reads and a bam file, I chose to handle this by testing if the channel exists (to differ between bam and reads), and the meta.single_end key to identify paired or single-end.

PR checklist

Closes #4307

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[mapo9]

Hi Joao @Joaodemeirelles,

thanks for your work in adding this module!
I am also very interested to have this and would have some time now to work on it.

Can you tell me what still needs to be done?

Also, did you think about implementing tests yet?

[mapo9]

Hi, I took this PR up again as I want to make use of the tool.

I experience some problems that I am unsure on how to deal with them.
First, nf-test fails as some files stay empty in the small test dataset. As linting failed due to md5sums for empty files, I removed the md5sums for these files. This made nf-test fail as the snapshots are now different due to the missing md5sums.

Also, singularity fails because there is no singularity container for the newest version of the tool and some output seems to have changed so the md5sums differ as well from the docker & conda run with the newest version.

Does anyone has an idea how to solve this?

[mapo9]

I was able to solve the problems above and think that the PR is now ready for review :)

[Joaodemeirelles]

I was able to solve the problems above and think that the PR is now ready for review :)

Great! Sorry I could not help with the tests, thank you so much for the changes!

[FriederikeHanssen]

we need meta1 and meta2 here. What is the difference between fasta and ref, how about: vdj_reference?

[mapo9]

ref is an additional reference required when you dont start from bam but fastq
fasta is what they call their reference basically.
I wanted to stay in line with their naming here, but am also fine with renaming them.

[ggabernet]

Looks good to me now! There's only the trinity pytest that I'm not sure they should be added here