Update Hifiasm to 0.19.9

[Schmytzi]

Bumped HifiAsm to 0.19.9. Also added tests.

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[sateeshperi]

Suggested change

	test("Test HifiAsm - fq [] [] [] []") {
	test("homo_sapiens pacbio hifi [fastq]") {

[sateeshperi]

are you leaving out any channel or could all out channels be captured with process.out ?

[Schmytzi]

I'm leaving out the log and the binary files as those are not stable. The latter aren't documented as output files either but I figured some people might depend on them and I did not want to change the process definition.

[sateeshperi]

optional outputs ?

[Schmytzi]

Yes, these are optional. Should I rather remove them from the test if we expect them to not be present?

[sateeshperi]

yes

[sateeshperi]

u need to rm pytests and fix the nf-tests. reach on #nf-test channel if you are stuck

[GallVp]

Thank you for the contribution.
The pytests are still running. Can you please delete the pytest files for hifiasm?

[fellen31]

This could be adressed in another PR, but since you are writing the tests:

The paternal and maternal kmer inputs (as well as the HiC inputs) are specific to the reads, and I think they should be input together, i.e.:

tuple val(meta), path(reads), path(paternal_kmer_dump), path(maternal_kmer_dump), path(hic_read1), path(hic_read2)

Otherwise, I think there's no way to ensure that the reads and kmers that belong together are input to the process together, so Sample1 could get Sample2's parental kmers.

[fellen31]

Could we update this straight to 0.20.0?

[Schmytzi]

I think there's value in having version 0.19.9 in at least one version of nf-core/modules. In part because there appear to be some major changes in 0.20. We could combine the update to that version with your suggested change of the input channel.

[fellen31]

I'll post it as a separate issue: #6799

[fellen31]

You will need to pass -f0 with a nextflow.config to hifiasm to reduce the RAM requirements, in order for the tests to run on the GitHub runners.

[Schmytzi]

Thanks for the hint! I was going crazy over that 😄

[mahesh-panchal]

Otherwise, I think there's no way to ensure that the reads and kmers that belong together are input to the process together, so Sample1 could get Sample2's parental kmers.

We usually use multiMap for this.