@Phil Ewels do we need to do anything with the website?

I suppose you can all add yourself to the repo? if you want to

I never doubted you, I'm just impressed, I'm not sure I would have done so well

nonsense 🙂 look at what you do with sarek

Gavin is visiting here in Pavia btw, we discussed a bit about subworkflows we should catch up after easter

(nothing to do with this channel :P)

Working on the website now

Pipeline page up: https://nf-co.re/hgtseq

About to run the repo settings automation

Do you need to do anything for the page to be up?

already got a first PR: https://github.com/nf-core/hgtseq/pull/1

ok, repo settings done 👍🏻

@Francesco Lescai please set a bunch of keywords for the repo:

(they're used for the search on the nf-core website)

Hello <!here> we’ve got our first major PR for this pipeline, and it should be in a reasonable shape to pave the way for the first release. https://github.com/nf-core/hgtseq/pull/4 it’s a crazy busy period and ahead of summer holidays, plus it’s a PR to dev, but if someone has time or curiosity to give it a look would be very much appreciated 🙂 until merging, a proper testing can be run from @Simone Carpanzano repo. we’ve tested it on local laptops, HPC, and AWS to prepare this PR. thanks! 🙏

Hi <!channel> we’re preparing a manuscript to present this pipeline, for submission in this special issue: https://www.mdpi.com/journal/ijms/special_issues/Data_Mining_Bioinformatics#info as usual, the initiative is open to anyone in this channel who would like to contribute: please do let me know if you’d like to participate and we can find the best way for those who are interested. Deadline for submission of the manuscript is October 24th. Currently, I’ve run the pipeline on 2 Human exome dataset, one mouse exome dataset and one macaca exome dataset. Each with 10-12 samples. I’m preparing a computing benchmark as well as comparison of the results. The idea is finalise the pipeline with a first release, ideally by the end of the Hackathon. This will be coordinated by @Simone Carpanzano Looking forward to hearing from you and progress on this!

I'm beginning review process now! I see you're getting a failure on branch protection though which is a bit wierd... https://github.com/nf-core/hgtseq/actions/runs/3243236834/jobs/5317657011 <!subteam^S016E36N7TQ> (or infrastructure members of...) any idea?

First release is live! https://twitter.com/nf_core/status/1584532636416069633

Wrapping up the post-release tasks now 👍

<!here> and <!subteam^S044DU0NG68> for those who are interested in reading the pre-print (and are not annoyed already with IJMS emails 😅 ) here’s the link to the pre-print on biorXiv, while we wait for the peer-review https://www.biorxiv.org/content/10.1101/2022.10.24.513588v1

<!channel> just to communicate the manuscript has been accepted for publication in the Section of Molecular Informatics of the International Journal of Molecular Sciences. I thought was worth sharing a couple of comments from the reviewers, particularly with <!subteam^S016E36N7TQ> and @Evan Floden because they really appreciated the added value of nf-core and tower. from the first reviewer:

the website provided by the authors is clearly guided and equipped with helpful instructions and manuals

and more from the second reviewer:

The workflow is seamless, and I am impressed with its implementation in nf-core which makes it very easy to generate JSON file for downstream analyses. The documentation at <https://github.com/nf-core/hgtseq> makes it easy to access the pipeline through multiple pipelines. I did try launching through all platforms. I found the Nextflow Tower really exciting as it allows one to use different compute environments, especially slurm which is used by many University clusters.

I’m not sure if this marks the first paper officially authored by

nf-core community

but I’d definitely congratulate Mr. Community as well, for the key part played in this 🙂

Has anyone tried running this pipeline recently? I tried running the hgtseq pipeline with the test data but I’m having trouble (see thread).

Hi! This pipeline didn't get a template update with tools 3.3.2 due to the missing value for

manifest.contributors

in the

nextflow.config

file. Please make sure to complete the template update for v3.3.1 and add the

contributors

field. You can read the blog post about the 3.3.1 template update and ping us if you encounter any problem. Once you changed that in your

dev

branch, you will be able to continue receiving template updates.

Hi, I can’t seem to get run this pipeline on Seqera platform, I’m getting this

Unable to parse pipeline config

error when I try to add the pipeline

can anyone run the pipeline with

test_full

profile? I can run the other test profiles fine but not this one I keep getting this error

ERROR ~ Unable to parse config file: '/home/pampum/.nextflow/assets/nf-core/hgtseq/nextflow.config'

  Compile failed for sources FixedSetSources[name='/groovy/script/Script72F019F11756EED5C88893293A405E06']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  /groovy/script/Script72F019F11756EED5C88893293A405E06: 15: Unexpected input: '{' @ line 15, column 8.
     params {
            ^
  
  1 error


 -- Check 'TESTS/TEST_OUTPUTS/20251105_120940/nextflow.log' file for details

There was a copy + paste syntax error - PR to fix here: https://github.com/nf-core/hgtseq/pull/54

There's a failing test because the GitHub actions are deprecated. Unfortunately it looks like this pipeline needs a bit of love on the template updates 🙄

And it'll now stop getting any more template updates after those because of this.

@Francesco Lescai any thoughts on maintenance for this pipeline? I wonder if we should consider archiving it if there is no-one realistically available to maintain it now (though clearly there is some interest in running it).

@Mark Pampuch I’ve used most of my free time this week to fix the issues I could spot and I’ve merged a PR to dev to: • make sure it runs on seqera platform (the issue was a silly missing space / newline between code and comment which doesn’t trigger an error in Nextflow but apparently does when Seqera platform parses the config) • a much more important fix to a Java NPE error, which only happens with versions 25.x of Nextflow (can’t figure out the reason, but it’s fixed) • full test run (I’ve tested on Seqera platform using our GCP environment, as well as local HPC): please notice here the R report has failed due to wall-time and I purposedly set the error strategy to

ignore

instead of

retry

. the report on the pipeline has always been intended to be more a parsing of the outputs rather than a proper analysis, due to the difficulty in generalising how people use the data • template has been updated to nf-core version 3.3.2 (which is not the latest one): there is still an impossible for me to understand linting error, which is only thrown in the PR github action and not in the

nf-core pipelines lint

run on the devcontainer, flagging a difference in the PR template file: this is irrelevant to pipeline functionality all of this is in dev, so if you wish to run from Seqera please make sure you select the

dev

branch or run Nextflow with

-r dev

besides all this maintenance stuff, we’re of course available to discuss any science-based collaboration of course.