Fixes #65

[evancofer]

This is a minor change to fix #65 . This error is caused whenever UMI deduplication is run. The error is due to the fact that BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME and BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME are not included or defined anywhere. They should be included by including BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS from the bam_dedup_stats_samtools_umitools workflow. A working version of this (with minor changes) is already in the nf-core rnaseq pipeline, which served as the template for many of these changes.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/riboseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[evancofer]

I see that the linting check failed, but it seems to run fine locally with nf-core 2.14.1 and nextflow 24.04.4.

[lpantano]

@evancofer sorry for the delay, can you add a note in the CHANGELOG.md about this, then I can work on merging, thanks!

[evancofer]

@lpantano I actually think there are still some bugs in this code. I don't have the bandwidth to fix this though, so you can close it if needed. IIRC I gave up on this, because it ended up being a little involved. I think the easiest way to fix the problem however would be just update the RNA-seq portion of this to use a more recent version of the RNA-seq pipeline that this is based off of. I think it worked fine when I used that.

[pinin4fjords]

Sorry to miss this earlier.

Maybe at this point we should start by copying wholesale the equivalent unit from rnaseq dev, and try from there. I think we may have had some changes in the meantime.

[pinin4fjords]

Suggested change

	ch_transcriptome_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
	ch_transcriptome_bai = BAM_SORT_STATS_SAMTOOLS.out.bai
	ch_transcriptome_sorted_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
	ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai

rnaseq does this (also rename the input to the function below), so that the unsorted bam is not over-written. Maybe try this first?

[iraiosub]

I opened a new PR #75 to solve the UMI issue.

[FelixKrueger]

This has now been addressed (see above), closing.