Keep that in mind for next release#

This looks like it's worth taking a look at: https://ga4gh.github.io/refget/seqcol/

@Maxime Garcia was reading the maintainer's minutes. It says that no-one is using igenomes.config, but don't most pipelines use it? It's the backbone of

--genome

that's pretty commonly used, right?

Hi all, for the references pipeline, we do have a milestone that is populated quite nicely. I will focus first on completing it and adding more issues

packing for the day, will do more tomorrow

Hi what is the purpose of the files on this line and all lines after that? https://github.com/nf-core/modules/blob/565c264868ccfe46a4c87a4ab3f812298c307597/subworkflows/nf-core/utils_references/schema_references.json#L42 (I'm trying to get a better understanding in order to update the JSON schema)

Have you already seen this announcement from GA4GH about refget Sequence Collections? Like every standard, it is a quite complicated document, but it could be an interesting addition to the pipeline to optionally query their API with the reference genome being processed and then create this unique hash? "_Seqcol also handles sequence attributes, such as their names, lengths, or topologies. Like Refget sequences, seqcol digests are defined by a hash algorithm, rather than an accession authority_" "_Seqcol also provides a standardized method of comparing the contents of two sequence collections_"

I was hoping to use this to build a STAR index for a mouse genome. I ran it and it didn't appear to actually do anything to build anything? Or am I running it wrong? I realize that this appears to be a 0.1 version, so I have low expectations.

We have a mild concern/observation about the file structure. When we build indices for a bunch of tools, some care about the transcripts and some don't. If we build a genome for a new GTF (say GENCODE 36 when we had 35 built), the genome.transcripts.fa that it generates is specific to the GTF, and there's nothing to indicate what it was based on. Or is this expecting to regenerate all of the references every time there's a new GTF?

Hi all, this is the poster I just presented at the Nextflow Summit in Boston

We now have a metro X-mas tree map for #C073ZDLNC92

<!here> after some thinking, discussions, thinking, I have a pretty good plan into making a transition from the current situation to what I think we should be doing for the #C073ZDLNC92. I am now looking for partners in crime, to help polish the multi-step plans, launch it and make it as easy as possible for the developers to implement, and without issues for the users (🧵 for the plan).

The way I see it, #C073ZDLNC92 is currently a small tree, getting bigger and bigger. By adding building #C073ZDLNC92 outside of genomics, for pipelines like #C084HP11VPF, we will add more trees, and #C073ZDLNC92 will become a full forest

Ping for an update on the status of the

dev

branch... love the map and logo, but does it work? 😉

I ran with the following input yaml file

- genome: GRCh38.p14
  fasta: <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz>
  gff: <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gff.gz>
  gtf: <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz>
  mito_name: MT
  source_version: GCF_000001405.40
  source: NCBI
  species: Homo_sapiens

and

--tools bwamem1,createsequencedictionary,dragmap,faidx,intervals,rsem,rsem_make_transcript_fasta,salmon,sizes,star,tabix

, which kinda worked, although rsem/star were unhappy with the GFF/GTF files. Are there any examples of putting together multiple sources into one input yaml file? I'm thinking specifically GRCh38.p14 plus GATK bundle for sarek and Ensembl and Encode for rnaseq rsem/star.

It does work

there are some things that needs to be ironed out

I might not have put in auto-extract for gtf/gff

Cool, I ran with some other GTF/GFF references over the weekend, I will check out the results later today

I have been caught up catching up some stuff in #C01NHS4CC91 #CGFUX04HZ and other pipelines, but I'll shift my focus back in here in a couple of days

Sorry, is this referring to the vep, snpEff (and bcfann?) annotation caches? https://github.com/nf-core/references/issues/104

In any case, this is the problem I ran into 4:02 PM

Hihi, slightly offtopic of the references pipeline but we were wondering if you potentially already have VEP annotation caches uploaded somewhere for CHM13 that can be pulled in a pipeline? We were wondering what the best way to host these things is

If people are done swooning over snpEff, Ensembl just dropped v115 with support for structural variant annotation from gnomAD 😉 conda recipe and docker image are already available

@Maxime Garcia We were wondering if the plans (in the future) are also to support Panel of Normals for CHM13 and long-read sequencing pipelines. We got some panel of normals that we want to use for tumour-only variant calling with ClairS-TO for instance that are too large to host on github. Maybe these can be hosted on aws and included in the end as well?

A little off-topic, is there a SBOM-like data standard for datasets? I'd like to create a bill of materials with file sizes and checksums for the output of an nf-core/references run so that I can more easily version it. #FAIR

I started working on SPDX but it doesn't fit genomic data very well (file size is an integer?? facepalm) https://spdx.github.io/spdx-spec/v3.0.1/model/Dataset/Classes/DatasetPackage/

Potentially interesting talk announcement for the #C073ZDLNC92 community: > Come along to learn about the European Reference Genome Atlas from Camila Mazzoni > > The European Reference Genome Atlas (ERGA), the European regional node of the Earth BioGenome Project, is an open initiative that aims to facilitate the generation of high-quality reference genomes for the continent’s biodiversity. ERGA acts as an umbrella for projects producing genomes from Europe’s biodiversity and brings together researchers and stakeholders to coordinate standardised sampling, sequencing, data management, assembly, and annotation for reference genomes across diverse groups of eukaryotes. Through projects like the ERGA Pilot Project and the Biodiversity Genomics Europe (BGE) project, as well as contributions from ERGA national nodes and the broader research community, ERGA aims to accelerate the generation and sharing of genomic resources that will contribute to future discoveries and genomics-based applications in ecology, evolution, bioeconomy, and conservation of species in Europe. > When? 11.12.2025 at 11 CET > Where? Zoom, register here: https://rwth.zoom-x.de/meeting/register/1PU7ZBhuSS-rYHG7PF5LGA

Hi, our lab has been using Nextflow for ATAC-seq and CUT&RUN that was done with chicken embryos. I was wondering if it would be possible for Nextflow to host the latest genome (Galgal6) as opposed to Galgal4 which is the only reference genome available currently. Much appreciate any help on this. Thanks!

I don't remember but has there been done any work on an actual references plugin? Strict syntax has changed some configuration parsing which makes the current way with

params.genomes

less easy to use. It would be better if we could just move this logic to a plugin and resolve everything on the workflow level instead