update bowtie2 v2.5.4

[LucilleAugusta]

PR checklist

Closes #6821

• [ x] This comment contains a description of changes (with reason).
• [ x] 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:
    • [ x] nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

For bowtie2/align the old mulled biocontainers have been changed to new Seqera containers.

[LucilleAugusta]

Hi
I'm having troubles figuring out why the bowtie2/align, singularity test is failing?

[fmalmeida]

Hi @LucilleAugusta ,
Looking at the error, although strange, it looks like for some reason, the lines collected are not exactly the same, probably due the order of some reads.

To try to solve that, I have changed the 'sorting' value to true in the nf-test file, so that we ensure to have always the same order, and then increased a little bit the amount of lines from output collected.

Let's see if this help. If so, something similar has to be done for the other tests that fail, if they actually relate to the changes you made. If they are of a different tool, then probably should not be of the scope of this PR.

[LucilleAugusta]

Thanks for taking a look @fmalmeida.

The tests failing seems to be related to subwokflows - fastq_align_dna and fastq_align_bowtie2.
It is not clear to me if this is related to I the changes I made.
Can you help me define the next steps?

[fmalmeida]

Hi @LucilleAugusta ,

I seems that the other workflows are just complaining in the versions.yml snapshot which makes sense since we updated the bowtie2 version.

So, probably just running them with --update-snapshot should do the trick.

😄

[nservant]

Looks good to me. Thanks

[edmundmiller]

Suggested change

	'oras://community.wave.seqera.io/library/bowtie2_samtools_pigz:19e9ad812f803021' :
	'oras://community.wave.seqera.io/library/bowtie2_samtools_pigz:19e9ad812f803021' :

We're not supporting oras yet. There's a script https://github.com/nf-core/modules/blob/master/.github/scripts/wave_singularity.py for this if anyone beats me to it, just going through Seqera container issues.

[SPPearce]

@LucilleAugusta , do you need help to get this finished off?