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# request-core
  • r
    A new request to activate Zenodo for a pipeline has been made! • Pipeline name: genomeqc Core team will activate Zenodo for this pipeline. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Fernando
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  • s
    A request to be added to nf-core Seqera Platform AWS Megatest workspace has been made! • Person name: Fernando Duarte • Account: d-fernando-fg • Pipeline name: genomeqc • Request confirmed: This pipeline has been accepted in nf-core through the proposal process Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @Fernando
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  • j
    Hi everyone! We are currently preparing the last steps for the first official release of nf-co.re/diseasemodulediscovery/dev For this, we migrated all containers to seqera or biocontainers, but for three of them, this is not possible, as the tools rely on unpackaged scripts, which need to be included into the containers. Because of this, we followed the instructions provided here: nf-co.re/docs/…/custom_containers The containers are now hosted on my personal docker hub and it would be amazing, if someone could transfer them to the official nf-core quay.io Thanks a lot in advance!
    Copy code
    # DIAMOnD
docker pull kerstingjohannes/diamond:1.0.0-2437974
docker tag  kerstingjohannes/diamond:1.0.0-2437974 <http://quay.io/nf-core/diamond:1.0.0-2437974|quay.io/nf-core/diamond:1.0.0-2437974>
docker push <http://quay.io/nf-core/diamond:1.0.0-2437974|quay.io/nf-core/diamond:1.0.0-2437974>

# ROBUST
docker pull kerstingjohannes/robust:1.0.0-e8861de
docker tag  kerstingjohannes/robust:1.0.0-e8861de <http://quay.io/nf-core/robust:1.0.0-e8861de|quay.io/nf-core/robust:1.0.0-e8861de>
docker push <http://quay.io/nf-core/robust:1.0.0-e8861de|quay.io/nf-core/robust:1.0.0-e8861de>

# BioPAX Validator
docker pull kerstingjohannes/biopax-validator:6.0.0
docker tag  kerstingjohannes/biopax-validator:6.0.0 <http://quay.io/nf-core/biopax-validator:6.0.0|quay.io/nf-core/biopax-validator:6.0.0>
docker push <http://quay.io/nf-core/biopax-validator:6.0.0|quay.io/nf-core/biopax-validator:6.0.0>
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  • d
    I'm in the process of preparing my 
    nf-core-sativa
    repo to be transferred to 
    nf-core/taxmarker
    . I will do the in-code renaming of the pipeline first, can you then rename the repo at the same time as you transfer ownership, or I should I rename the repo?
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  • d
    github.com/erikrikarddaniel/nf-core-sativa is now ready to be transferred to nf-core as taxmarker. Approved as an nf-core pipeline. Renaming of code has so far only touched 
    dev
    , not 
    master
    . Let me know if you want me to do that too. I wouldn't mind becoming an admin.
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  • v
    Hi <!subteam^S016E36N7TQ> my pipeline nf-core/rnastructurome has now been approved by 3 people including a core member but I still can't merge the PR. Can anyone tell me what I need to do now? Thank you! github.com/nf-core/rnastructurome/pull/5
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  • t
    A new request to upload a dataset to nf-core AWS S3 bucket has been made! • Requested by: @Niklas Schandry • Pipeline name: genomeassembler • Why is this needed?: This is HiC test data for genomeassembler • Size of the dataset: 5,749.57 MB for _1 and 6,069.85 MB for _2 • URL: GSA browers: https://ngdc.cncb.ac.cn/gsa/browse/CRA004538/CRR302669 Direct file (https) https://download.cncb.ac.cn/gsa/CRA004538/CRR302669/CRR302669_f1.fastq.gz https://download.cncb.ac.cn/gsa/CRA004538/CRR302669/CRR302669_r2.fastq.gz • Related files: Core team will add this dataset to the nf-core bucket. Please react to the message with ✅ when this is done. [This process is not automated]
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  • r
    A new request to activate Zenodo for a pipeline has been made! • Pipeline name: rnastructurome Core team will activate Zenodo for this pipeline. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Victoria Begley
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  • f
    Hi! I'm trying to finish the post-release tasks for #C07LY51P4S2, and I have a few requests and questions: • My AWS Megatest is failing cloud.seqera.io/orgs/…/logs. I'm not sure what's exactly the problem, since the file that apparently can't be staged does exist. I opened a thread in the AWS megatests channel about this: https://nfcore.slack.com/archives/CTY8L26C8/p1788338290104469. • About this section in nf-core's release procedure: "Ask on the #C09H6NYHR9T channel to add on the 
    main
    branch the new DOI to the 
    nextflow.config
    manifest, the badge to top of the the 
    README.md
    , and update the 
    Citation
    section of the `README.md`"    . We have a pre-print - the DOI is 10.64898/2026.08.20.745971. Is it okay if we use this DOI instead of the automatically generated Zenodo one? If so, can someone add it? • Can someone change the fault branch from 
    dev
    to 
    main
    ?
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  • l
    Hi, I've been trying to make 
    UNIVERSC
    works with singularity but the cellranger executable in quay.io/nf-core/universc:1.2.5.1 is in a non writable location. Does anybody know how I could fix this directly in the container ? 
    --writable-tmpfs
    doesn't work due to underlay.
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    WARNING: Disabling --writable-tmpfs as it can't be used in conjunction with underlay
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  • n
    Hi all, how do I create a tag for a release? I can't do it locally 
    ! [remote rejected] 1.0.0 -> 1.0.0 (push declined due to repository rule violations)
    and I can't do it via the web
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    Tag could not be created. Pre-receive hooks failed. repository rule violations found

Cannot create ref due to creations being restricted.
    ` Thread in Slack conversation
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  • r
    A new request to upload a container to quay.io has been made! • Container URL: Instructions to build at https://github.com/nf-core/modules/tree/master/modules/nf-core/cellranger#readme • Why is this needed?: Update cellranger from version 10.0.0 to 10.1.0 • Confirmation: ◦ This can't be done through the usual Bioconda Note: only containers with a stable version will be accepted (ie. not 
    latest
    ) Core team will add this container to quay.io. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Michael Heuer
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  • r
    A new request to activate Zenodo for a pipeline has been made! • Pipeline name: tumourevo Core team will activate Zenodo for this pipeline. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Lucrezia Valeriani
    ✅ 1
  • s
    A request to be added to nf-core Seqera Platform AWS Megatest workspace has been made! • Person name: Lucrezia Valeriani • Account: valerianilucrezia11 • Pipeline name: tumourevo • Request confirmed: This pipeline has been accepted in nf-core through the proposal process Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @Lucrezia Valeriani
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  • r
    A new request to activate Zenodo for a pipeline has been made! • Pipeline name: stableexpression Core team will activate Zenodo for this pipeline. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @oliviercoen
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  • s
    A request to be added to nf-core Seqera Platform AWS Megatest workspace has been made! • Person name: Olivier Coen • Account: olivier-coen • Pipeline name: stableexpression • Request confirmed: This pipeline has been accepted in nf-core through the proposal process Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @oliviercoen
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  • t
    A new request to upload a dataset to nf-core AWS S3 bucket has been made! • Requested by: @Daniel Lundin • Pipeline name: metatdenovo • Why is this needed?: Databases for annotation. I'm actually not certain what makes sense in tests. The Kofamscan database is the most important and the one we use in our projects for functional annotation. The dbCAN is less important. The only functional annotation done by the full scale tests today is the quite outdated eggNOG-mapper against v. 5 of the eggNOG database. I think we chose this because it was already uploaded. 1. dbCAN to 
    <s3://ngi-igenomes/test-data/metatdenovo/dbcan/dbcan_db/>
    . The last full test downloaded it but couldn't write it there (403). A copy should still be in 
    <s3://nf-core-awsmegatests/work/metatdenovo/work-dev/9d/a7d3c1b25a8fc0407b25e0bf458351/dbcan_db/>
    (about 5–6 GB); otherwise 
    run_dbcan database --no-cgc --db_dir dbcan_db --aws_s3
    (dbCAN 5.2.9) recreates it. 2. KOfamScan to `s3://ngi-igenomes/test-data/metatdenovo/kofam/`: 
    ko_list
    (unzipped from https://www.genome.jp/ftp/db/kofam/ko_list.gz) and the 
    profiles/
    directory (unpacked from https://www.genome.jp/ftp/db/kofam/profiles.tar.gz). • Size of the dataset: 14 and 8 GB respectively • URL: See instructions above. • Related files: Core team will add this dataset to the nf-core bucket. Please react to the message with ✅ when this is done. [This process is not automated]
  • l
    While trying to create a new release, the tag creation failed with this error:
    Copy code
    Tag could not be created. Pre-receive hooks failed.
Repository rule violations found

Cannot create ref due to creations being restricted.
    I'm using the tag 
    1.0.0
    . I think you have to remove the protection? Thank you in advance!
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  • s
    A request to be added to nf-core Seqera Platform AWS Megatest workspace has been made! • Person name: Bilal Asser • Account: asserbbioinfoprojects@gmail.com • Pipeline name: pathogenepidemiology • Request confirmed: This pipeline has been accepted in nf-core through the proposal process Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @Bilal Asser
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  • r
    A new request to activate Zenodo for a pipeline has been made! • Pipeline name: datasync Core team will activate Zenodo for this pipeline. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Delfina Terradas
    ✅ 1
  • r
    A new request to upload a container to quay.io has been made! • Container URL: wave.seqera.io/wt/31a6e5f54e99/wave/build:b9dbc80cb5dd84ee • Why is this needed?: This is the universc container. https://github.com/nf-core/modules/pull/12955 I would like to push the docker as well as the converted singularity image (to avoid OCI conversion). I tried 
    wave -i <http://wave.seqera.io/wt/31a6e5f54e99/wave/build:b9dbc80cb5dd84ee|wave.seqera.io/wt/31a6e5f54e99/wave/build:b9dbc80cb5dd84ee> --singularity --freeze --build-repository <http://quay.io/nf-core/universc|quay.io/nf-core/universc> --tower-token=$TOWER_ACCESS_TOKEN
    but this result in a failed container build/ • Confirmation: ◦ This can't be done through the usual Bioconda Note: only containers with a stable version will be accepted (ie. not 
    latest
    ) Core team will add this container to quay.io. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Louis Le Nézet
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  • r
    A new request to activate Zenodo for a pipeline has been made! • Pipeline name: plasmodiumdrugres Core team will activate Zenodo for this pipeline. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @kathryn.murie
    ✅ 1
  • t
    A new request to upload a dataset to nf-core AWS S3 bucket has been made! • Requested by: @piplus2 • Pipeline name: rnasplice • Why is this needed?: Full size tests • Size of the dataset: 129 GB • URL: s3://ngi-igenomes/test-data/rnasplice/ • Related files: Core team will add this dataset to the nf-core bucket. Please react to the message with ✅ when this is done. [This process is not automated]
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  • s
    A request to be added to nf-core Seqera Platform AWS Megatest workspace has been made! • Person name: Paolo Inglese • Account: p.inglese@outlook.com • Pipeline name: rnasplice • Request confirmed: This pipeline has been accepted in nf-core through the proposal process Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @piplus2
    ✅ 1
  • u
    A request to unblock releases has been made! • Person name: James • Pipeline name: #C071K9XPF47 • Request confirmed: Pipeline first release has two approvals (min. from 1 core/maintainer team) Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @James Fellows Yates
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  • t
    A new request to upload a dataset to nf-core AWS S3 bucket has been made! • Requested by: @Adrien Coulier • Pipeline name: nf-core/pixelator • Why is this needed?: Running AWS full tests. This is data from an internal run. We'll need to figure out a way to transfer it over to you. Our suggestion is to put it on our own FTP platform, so that someone from the core team can download it and upload it on the nf-core s3 bucket • Size of the dataset: 58.4 GiB • URL: See above • Related files: Core team will add this dataset to the nf-core bucket. Please react to the message with ✅ when this is done. [This process is not automated]
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  • u
    A request to unblock releases has been made! • Person name: Kathryn • Pipeline name: #C08AL3N8R5Y • Request confirmed: Pipeline first release has two approvals (min. from 1 core/maintainer team) Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @kathryn.murie
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  • s
    A request to be added to nf-core Seqera Platform AWS Megatest workspace has been made! • Person name: Kathryn • Account: kathryn-murie • Pipeline name: plasmodiumdrugres • Request confirmed: This pipeline has been accepted in nf-core through the proposal process Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @kathryn.murie
    ✅ 1
  • s
    A request to be added to nf-core Seqera Platform AWS Megatest workspace has been made! • Person name: Igiraneza Clément • Account: igiraclement@gmail.com • Pipeline name: nf-core/pathogenepidemiology • Request confirmed: This pipeline has been accepted in nf-core through the proposal process Next steps: 1. Someone from the core team add you to the organisation The core team member will react to the message with ✅ when this is done. [This process is not automated] submitter: @IGIRANEZA CLEMENT
    ✅ 1