Add fq2bam fq align dd bwamem

[eduard-watchmaker]

PR checklist

Closes #XXX

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[Joon-Klaps]

The changes in nf-test.config is something that needs to be double checked.

[eduard-watchmaker]

The changes in nf-test.config is something that needs to be double checked.

Removed and added to specific subworkflow tests directives!

[Joon-Klaps]

Sorry, quite a few things I should have spotted in the first round.

[eduard-watchmaker]

The Channel.empty() works with my tests, the mentioned [[:], [] ] did not, so I kept as it.

Thanks again for your time and review.

[eduard-watchmaker]

@Joon-Klaps any thoughts on the state of the branch?

[Joon-Klaps]

@nf-core-bot update gpu snapshot path: subworkflows/nf-core/fastq_align_dedup_bwamem

[Joon-Klaps]

@eduard-watchmaker, seems like the gpu snapshot files are still empty. This is likely becuase you've provided Channel.empty() as an input. Whenever a nextflow process recevies an Channel.empty(), it doesn't get executed. There is a difference between Channel.of([[:], []]) and Channel.empty().

I'm suprised to hear that [[:], []] didn't work, as it's the default way of providing empty inputs. Why didn't it work?

Also you didn't adress this https://github.com/nf-core/modules/pull/9309/files#r2485746222.

[eduard-watchmaker]

@eduard-watchmaker, seems like the gpu snapshot files are still empty. This is likely becuase you've provided Channel.empty() as an input. Whenever a nextflow process recevies an Channel.empty(), it doesn't get executed. There is a difference between Channel.of([[:], []]) and Channel.empty().

I'm suprised to hear that [[:], []] didn't work, as it's the default way of providing empty inputs. Why didn't it work?

Also you didn't adress this https://github.com/nf-core/modules/pull/9309/files#r2485746222.

I keep getting the:
Caused by:
Path value cannot be null

but that may actually not be the reason of it, although I can't find the culprit at all.

[Joon-Klaps]

Your variables are not passed correcty,
How it's written within the subworkflow:

ch_reads // channel: [ val(meta), [ reads ] ]
ch_fasta // channel: [ val(meta), [ fasta ] ]
ch_fasta_index // channel: [ val(meta), [ fasta index ] ]
ch_bwamem_index // channel: [ val(meta), [ bwam index ] ]
skip_deduplication // boolean: whether to deduplicate alignments
use_gpu // boolean: whether to use GPU or CPU for bwamem alignment
output_fmt // string: output format for parabricks fq2bam (e.g., 'bam' or 'cram')
interval_file // channel: [ val(meta), [ interval file ] ]
known_sites // channel: [ val(meta), [ known sites ] ]

Outfmt comes before interval_file & known sites

[eduard-watchmaker]

thanks, that totally went under my radar!

[eduard-watchmaker]

fixed, still get error:
Caused by:
Path value cannot be null

maybe bwa_index is nmot working, I need to explore and debug more, any ideas welcome!

[famosab]

Ah yes the bwa/index issue I suspect. See github.com//issues/9230 for the ongoing discussion.

[famosab]

Should this not be the meth version then?

[eduard-watchmaker]

Sorry why would this be the meth version? We want the bwamem version to align normal DNA

[famosab]

Because of the comment a few lines below that :)

[eduard-watchmaker]

Ah yes the bwa/index issue I suspect. See github.com//issues/9230 for the ongoing discussion.

I assume these tests were running on the original version of fq2bam? Unsure why they are not working now with the samew bwa mem issue.