this can also help report navigation in drop https://github.com/nf-core/seqinspector/pull/135

Hi, I updated the intermediate files and now only one test fails. I am trying to run

tests/aberrant_splicing.nf.test

using

nf-test

but get the following error:

* Missing required parameter(s): input, genome

Any ideas on why this could happen? I am simply running this command:

nf-test test tests/aberrant_splicing.nf.test --profile docker --update-snapshot

I have a small pr fixing a bug in sex-matching algorithm. Anyone around to review it?

HAPPY NEW YEAR! I have another small pr. Anyone around to take a look?

With this one I think we are ready for a release @Nicolas Vannieuwkerke, @Drew Behrens.

I'm testing the pipeline now. I was wondering why the logic for groups is different from snakemake version. i.e.:

ae_groups           // list:          A list of groups to exclude from the aberrant expression analysis

We exclude the groups here.

Hi @Nicolas Vannieuwkerke, regarding the test data, turns out that one of our colleges has already aligned 120 of the samples from 1000-genomes-project and we have the bam files ready on our clusters. What is the status on your side? if you haven't started maybe we can simply use them?

I updated the pipeline to be strict syntax compatible: https://github.com/nf-core/drop/pull/97 anyone around to take a look at it?

Hi @Nicolas Vannieuwkerke, what is the status of the tests? are we close to the release? :))

Hi @Nicolas Vannieuwkerke @Yun Wang, I’m reaching out from a research group based in Phoenix, Arizona (USA). Our team works primarily on rare disease genomics, and we’re currently preparing to analyze a cohort of ~350+ samples using the DROP pipeline with Nextflow. We are interested in looking at aberrant alternative splicing events using RNASeq. While looking through the repository, we noticed that the pipeline is still under active development. We were wondering if there is an approximate timeline for the release. Since we’re planning to use it for a fairly large dataset, we’d be very happy to help test the pipeline and contribute in any way that might be useful before the release, whether that’s testing on real datasets, reporting issues, documentation improvements, or helping with small fixes. Please let us know if there’s anything where additional users/testers could be helpful. We’d be glad to contribute to the project. Thanks for all the work you’ve put into building and maintaining DROP!

anyone around to check a small but important pr? it fixes a bug in counting step of aberrant expression module. https://github.com/nf-core/drop/pull/98

@Ata Jadid Ahari could you finish your review of this PR? https://github.com/nf-core/drop/pull/94 This one is holding up the release 😛

Going through issues now, do we not have the exporting counts scripts ported over?

One small version bump and then the release PR should be ready for review: https://github.com/nf-core/drop/pull/100

Can I get a review? https://github.com/nf-core/drop/pull/102

One more small review: https://github.com/nf-core/drop/pull/103 getting there for the release 🤞

Last small fix needed before the pipeline is ready for a release review: https://github.com/nf-core/drop/pull/104

Some small changes in readme https://github.com/nf-core/drop/pull/105

@Ata Jadid Ahari we have enough approvals to push the release! Is there anything else missing from your side?

<!here> we have release 🐕 https://github.com/nf-core/drop/releases/tag/1.0.0 Thanks to everyone for helping to convert this pipeline!

A small PR to bump the version back to dev: https://github.com/nf-core/drop/pull/109

And another to add the zenodo DOI to the master branch: https://github.com/nf-core/drop/pull/110

<!here> Thanks so much for pushing the release. Super happy and grateful to all contributors @Nicolas Vannieuwkerke @Ata Jadid Ahari @Yun Wang especially

I got a small fix ready for some bugs I found: https://github.com/nf-core/drop/pull/113

I'm also seeing this error in `SPLICECOUNTS_COUNTSPLITREADS`:

Error in reducer$value.cache[[as.character(idx)]] <- values :
    wrong args for environment subassignment
  Calls: countSplitReads ... .bploop_impl -> .collect_result -> .reducer_add -> .reducer_add
  In addition: Warning message:
  In parallel::mccollect(wait = FALSE, timeout = 1) :
    1 parallel job did not deliver a result
  Execution halted

Anyone any ideas?

Hey all - thanks so much for the amazing work in translating the pipeline to nextflow! I would love to test in the Genomics England environment - just wondering if there is already an AWS batch profile we can use for execution?

Anyone around to check this? https://github.com/nf-core/drop/pull/115

<!here> anyone volunteering here to help out @Nicolas Vannieuwkerke to present the drop pipeline, he can cover the nextflow/nf-core part, but someone with a deeper understanding of the logic would be nice

Sadly couldnt make it for the bytesize but was wondering if this is exclusively for shot-read RNAseq or also works for long-reads?

Hi all, I’d just want to say thank you for porting the pipeline! I was able to finish most of the pipeline based on your guide here with our data. But the last MultiQC never finished, despite letting the step run for 18h+, with memory usage reaching up to 280 GB. So I eventually stopped the pipeline. I don’t know if this is a problem with MultiQC itself? And if so, is this still necessary to keep it?