# \#nf-core **URL:** https://community.seqera.io/tag/nf-core/42.md [Latest](https://community.seqera.io/latest.md) · [Categories](https://community.seqera.io/categories.md) · [Tags](https://community.seqera.io/tags.md) --- ## [Nextflow Training Week, September 2026](https://community.seqera.io/t/nextflow-training-week-september-2026/2739)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 11\ **Last updated:** [August 11, 2026, 11:12pm UTC](https://community.seqera.io/t/nextflow-training-week-september-2026/2739 "2026-08-11T23:12:31Z")
Nextflow Training Week: Self-Paced Online Training from the Nextflow Creators :technologist: :student: Looking to get started with Nextflow? Join us for our September Nextflow Training Week! This self-paced online traini… --- ## [How to properly add cellrangermulti vdj reference](https://community.seqera.io/t/how-to-properly-add-cellrangermulti-vdj-reference/2734)
**Author:** [@marcelcosta](https://community.seqera.io/u/marcelcosta)\ **Replies:** 1\ **Last updated:** [July 27, 2026, 8:54am UTC](https://community.seqera.io/t/how-to-properly-add-cellrangermulti-vdj-reference/2734 "2026-07-27T08:54:40Z")
Hi! I am trying to use scrnaseq pipeline for GEX+TCR analysis with cellranger multi pipeline. I am struggling with the VDJ reference parameters. This is my launcher command: NXF\_VER=25.10.4 nextflow run nf-core/scrnas… --- ## [Using local reference instead of connecting to iGenome](https://community.seqera.io/t/using-local-reference-instead-of-connecting-to-igenome/2724)
**Author:** [@marcelcosta](https://community.seqera.io/u/marcelcosta)\ **Replies:** 2\ **Last updated:** [July 22, 2026, 1:07pm UTC](https://community.seqera.io/t/using-local-reference-instead-of-connecting-to-igenome/2724 "2026-07-22T13:07:32Z")
Hi! I am trying to run “scRNAseq” nf-core pipeline with that command: NXF\_VER=25.10.4 nextflow run nf-core/scrnaseq \\ -profile test \\ --aligner cellranger \\ --fasta ~/Shared-MarcelCosta/apps/cellranger-10.0… --- ## [HackNatal 2026 - nf-core Hackathon in Brazil](https://community.seqera.io/t/hacknatal-2026-nf-core-hackathon-in-brazil/2720)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 0\ **Last updated:** [July 10, 2026, 8:55am UTC](https://community.seqera.io/t/hacknatal-2026-nf-core-hackathon-in-brazil/2720 "2026-07-10T08:55:16Z")
HackNatal 2026 - nf-core Hackathon in Brazil :brazil: :woman\_technologist: Register now An in-person hackathon to contribute to tasks related to nf-core and its Nextflow projects. This Hackathon will take place as part… --- ## [Best way to check the registry for modules that run a specific data processing command-line program](https://community.seqera.io/t/best-way-to-check-the-registry-for-modules-that-run-a-specific-data-processing-command-line-program/2685)
**Author:** [@aloraine](https://community.seqera.io/u/aloraine)\ **Replies:** 1\ **Last updated:** [May 22, 2026, 9:43pm UTC](https://community.seqera.io/t/best-way-to-check-the-registry-for-modules-that-run-a-specific-data-processing-command-line-program/2685 "2026-05-22T21:43:03Z")
Hi! Thanks for the great training materials! What’s the best way to check the registry for modules that run a specific data processing command-line program? For reference, I am interested in this one: Here also is … --- ## [Can I use other git hosting service and still support nextflow pull actions?](https://community.seqera.io/t/can-i-use-other-git-hosting-service-and-still-support-nextflow-pull-actions/2684)
**Author:** [@aloraine](https://community.seqera.io/u/aloraine)\ **Replies:** 1\ **Last updated:** [May 21, 2026, 8:07pm UTC](https://community.seqera.io/t/can-i-use-other-git-hosting-service-and-still-support-nextflow-pull-actions/2684 "2026-05-21T20:07:34Z")
Hi! I have a question about the nextflow pull command. Does it only work with github or can I use other git hosting services to distribute my work? Thanks! Ann L. --- ## [Issue with nextflows vs code parser reading my .venv file](https://community.seqera.io/t/issue-with-nextflows-vs-code-parser-reading-my-venv-file/2611)
**Author:** [@David\_Mas\_Ponte](https://community.seqera.io/u/David_Mas_Ponte)\ **Replies:** 3\ **Last updated:** [May 20, 2026, 9:32am UTC](https://community.seqera.io/t/issue-with-nextflows-vs-code-parser-reading-my-venv-file/2611 "2026-05-20T09:32:44Z")
Hi, I have a uv venv in my pipelines for running nf-core directly there. Note that this generates a .venv folder with all the packages when you run uv run sync. I have the nextflow extension installed in vs code (1.6.1… --- ## [Line of code in Training \> nf-core \> part 2 \> 1.2 fails on me](https://community.seqera.io/t/line-of-code-in-training-nf-core-part-2-1-2-fails-on-me/2637)
**Author:** [@m-d-grunnill](https://community.seqera.io/u/m-d-grunnill)\ **Replies:** 17\ **Last updated:** [May 15, 2026, 1:41pm UTC](https://community.seqera.io/t/line-of-code-in-training-nf-core-part-2-1-2-fails-on-me/2637 "2026-05-15T13:41:15Z")
I am running the training using the GitHub Codespace you provided ( Sign in to GitHub · GitHub ). In \[Training \> nf-core \> part 2 \> 1.2\](Part 2: Rewrite Hello for nf-core - training.nextflow.io) the line nextflow run .… --- ## [Nextflow Training Week: Self-Paced Online Training, From the Creators of Nextflow](https://community.seqera.io/t/nextflow-training-week-self-paced-online-training-from-the-creators-of-nextflow/2631)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 1\ **Last updated:** [May 11, 2026, 10:28am UTC](https://community.seqera.io/t/nextflow-training-week-self-paced-online-training-from-the-creators-of-nextflow/2631 "2026-05-11T10:28:51Z")
Join us for our second Nextflow Training Week of 2026! Whether you’re completely new to workflow management or ready to advance your skills, this flexible training offers something for everyone. Featuring on-demand walk… --- ## [Hello nf-core training part 4: ext.args is not taking the defined option](https://community.seqera.io/t/hello-nf-core-training-part-4-ext-args-is-not-taking-the-defined-option/2605)
**Author:** [@edipcorreia](https://community.seqera.io/u/edipcorreia)\ **Replies:** 1\ **Last updated:** [April 17, 2026, 8:01pm UTC](https://community.seqera.io/t/hello-nf-core-training-part-4-ext-args-is-not-taking-the-defined-option/2605 "2026-04-17T20:01:59Z")
Hey everyone, I’m following the Hello nf-core training tutorial and am now on Part 4: Make an Nf-core module (working in the provided GitHub codespace). After implementing ext.args in the COWPY module and in the HELLO … --- ## [ISMB Nextflow Tutorial - Hello nf-core](https://community.seqera.io/t/ismb-nextflow-tutorial-hello-nf-core/2628)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 0\ **Last updated:** [March 31, 2026, 2:31pm UTC](https://community.seqera.io/t/ismb-nextflow-tutorial-hello-nf-core/2628 "2026-03-31T14:31:57Z")
Hello nf-core: Level up your workflows with community-curated best practices and developer resources :green\_apple: Learn more This tutorial is designed for learners who have some familiarity with Nextflow and want to bu… --- ## [Nf-core Hackathon in Boston](https://community.seqera.io/t/nf-core-hackathon-in-boston/2625)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 0\ **Last updated:** [March 25, 2026, 3:02pm UTC](https://community.seqera.io/t/nf-core-hackathon-in-boston/2625 "2026-03-25T15:02:55Z")
Join the nf-core Hackathon in Boston this April! :green\_apple: Register to attend Hackathon | Nextflow Summit 2026 The nf-core hackathons are not competitive. Instead, they are collaborative, community-driven events… --- ## [Will map process inputs synchrously maintaining order?](https://community.seqera.io/t/will-map-process-inputs-synchrously-maintaining-order/2610)
**Author:** [@David\_Mas\_Ponte](https://community.seqera.io/u/David_Mas_Ponte)\ **Replies:** 3\ **Last updated:** [March 16, 2026, 2:03pm UTC](https://community.seqera.io/t/will-map-process-inputs-synchrously-maintaining-order/2610 "2026-03-16T14:03:58Z")
Hi, I have this bit of code generated by AI this morning and I am trying to double check if it is correct. Also looking for some sort of documentation I can link here when my future self tries to blame this on me. c… --- ## [How 'ignore' errorStrategy actually works?](https://community.seqera.io/t/how-ignore-errorstrategy-actually-works/2581)
**Author:** [@legezam](https://community.seqera.io/u/legezam)\ **Replies:** 4\ **Last updated:** [March 8, 2026, 4:16pm UTC](https://community.seqera.io/t/how-ignore-errorstrategy-actually-works/2581 "2026-03-08T16:16:14Z")
Hello, It seems that I am totally confused by how the ‘ignore’ errorStrategy is supposed to work. According to the documentation, I thought if i set it to ignore, the pipeline will continue to work. However, I have a si… --- ## [Alphafold using Nextflow - Azure Batch Executor DB staging issue](https://community.seqera.io/t/alphafold-using-nextflow-azure-batch-executor-db-staging-issue/2580)
**Author:** [@venkatt007](https://community.seqera.io/u/venkatt007)\ **Replies:** 0\ **Last updated:** [February 18, 2026, 6:18pm UTC](https://community.seqera.io/t/alphafold-using-nextflow-azure-batch-executor-db-staging-issue/2580 "2026-02-18T18:18:46Z")
Azure Batch + nf-core/proteinfold: AlphaFold DB Files Always Staging (Even with blobfuse2 Mounts) Hi all, I’m running nf-core/proteinfold (v1.1.1) on Azure Batch using the azurebatch executor in closed private network,… --- ## [Nf-core Hackathon - Online & In-Person](https://community.seqera.io/t/nf-core-hackathon-online-in-person/2574)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 0\ **Last updated:** [February 18, 2026, 8:22am UTC](https://community.seqera.io/t/nf-core-hackathon-online-in-person/2574 "2026-02-18T08:22:59Z")
The nf-core Hackathon returns on Mar 11-13, 2026 :green\_apple:- A hybrid hackathon to develop nf-core together. A hybrid hackathon to develop nf-core together Whether you’re new to nf-core or already involved with the… --- ## [Best practices for error handling in Nextflow](https://community.seqera.io/t/best-practices-for-error-handling-in-nextflow/2557)
**Author:** [@magletdinov](https://community.seqera.io/u/magletdinov)\ **Replies:** 1\ **Last updated:** [February 13, 2026, 3:12pm UTC](https://community.seqera.io/t/best-practices-for-error-handling-in-nextflow/2557 "2026-02-13T15:12:17Z")
Hello everyone! Could you please tell me any best practices for writing Nextflow code to flexibly configure pipeline error handling? If the samples are OK and the pipeline runs without failures, then the scenarios from… --- ## [Runnig Nextflow Chipseq](https://community.seqera.io/t/runnig-nextflow-chipseq/2555)
**Author:** [@Taimor\_Williams](https://community.seqera.io/u/Taimor_Williams)\ **Replies:** 2\ **Last updated:** [February 13, 2026, 12:23am UTC](https://community.seqera.io/t/runnig-nextflow-chipseq/2555 "2026-02-13T00:23:27Z")
Hi everyone! My name is Taimor I am a bionformatics RA at BCH. I am trying to run Nextflow chipseq pipeline for some of the researchers in my lab and am encountering some issuses. Currently the error i’m getting is rela… --- ## [Github codespace hello-nf-core import nf-schema error](https://community.seqera.io/t/github-codespace-hello-nf-core-import-nf-schema-error/2547)
**Author:** [@MartonHorvath98](https://community.seqera.io/u/MartonHorvath98)\ **Replies:** 4\ **Last updated:** [February 11, 2026, 8:42pm UTC](https://community.seqera.io/t/github-codespace-hello-nf-core-import-nf-schema-error/2547 "2026-02-11T20:42:48Z")
Hi! I have just started the hello-nf-core path, participating in the Training week. I have tried launching the nf-core demo pipeline, but the run failed with the following error message: A workflow named ‘UTILS\_NFSCHEMA… --- ## [Nextflow Summit Boston 2026](https://community.seqera.io/t/nextflow-summit-boston-2026/2548)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 0\ **Last updated:** [February 11, 2026, 5:15pm UTC](https://community.seqera.io/t/nextflow-summit-boston-2026/2548 "2026-02-11T17:15:37Z")
Registration is officially open for Nextflow Summit Boston 2026! Register now :tada: Join us on Apr 28 - May 1 for the premier gathering of the Nextflow community. :admission\_tickets:Register now The Nextflow Summi… --- ## [Hello-nf-core training codespace: plugin does not exist](https://community.seqera.io/t/hello-nf-core-training-codespace-plugin-does-not-exist/2521)
**Author:** [@benwinog](https://community.seqera.io/u/benwinog)\ **Replies:** 3\ **Last updated:** [February 8, 2026, 12:14am UTC](https://community.seqera.io/t/hello-nf-core-training-codespace-plugin-does-not-exist/2521 "2026-02-08T00:14:58Z")
Hi all, I am trying to follow Part 1 of the Hello nf-core training module in the provided GitHub Codespace. I am able to successfully pull the demo pipeline, but when I go to run the pipeline with the test profile as in… --- ## [Suggestion for getting people to review massive \`nf-core/pacvar\` PR](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525)
**Author:** [@chaochaowong](https://community.seqera.io/u/chaochaowong)\ **Replies:** 4\ **Last updated:** [February 4, 2026, 11:17pm UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525 "2026-02-04T23:17:56Z")
I’ve opened a PR for the nf-core/pacvar pipeline on the dev branch: After requesting help in the Slack #pacvar and #review-request channels, I haven’t been able to get feedback for over two weeks. I suspect the main is… --- ## [Pipeline PR issues with unstable llms-full.txt and multiqc.parquet](https://community.seqera.io/t/pipeline-pr-issues-with-unstable-llms-full-txt-and-multiqc-parquet/2513)
**Author:** [@chaochaowong](https://community.seqera.io/u/chaochaowong)\ **Replies:** 2\ **Last updated:** [January 21, 2026, 5:49pm UTC](https://community.seqera.io/t/pipeline-pr-issues-with-unstable-llms-full-txt-and-multiqc-parquet/2513 "2026-01-21T17:49:21Z")
My PR #42 (Add variant calls and methylation features, update modules, compliance with \`nf-core/tools\` template 3.5.1 by chaochaowong · Pull Request #42 · nf-core/pacvar · GitHub) for the pacvar pipeline has error with n… --- ## [Nextflow Podcast Ep. 53: Highlights form 2025](https://community.seqera.io/t/nextflow-podcast-ep-53-highlights-form-2025/2507)
**Author:** [@ewels](https://community.seqera.io/u/ewels)\ **Replies:** 0\ **Last updated:** [January 16, 2026, 12:50am UTC](https://community.seqera.io/t/nextflow-podcast-ep-53-highlights-form-2025/2507 "2026-01-16T00:50:45Z")
Hey everyone! :wave: The Nextflow Podcast is back! :tada: :nextflow: :studio\_microphone: After an extended hiatus in the second half of 2025 (house renovations - don’t ask), Episode 53 kicks off 2026 with a compreh… --- ## [ERROR ~ No such variable: ch\_multiqc\_report when trying to skip multiqc](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494)
**Author:** [@sky5198](https://community.seqera.io/u/sky5198)\ **Replies:** 5\ **Last updated:** [January 11, 2026, 11:52pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494 "2026-01-11T23:52:52Z")
I am trying processing ChIP-sequencing data using Nextflow. I am trying to skip the multiqc step as it is giving me some trouble by adding the --skip\_multiqc parameter to the command line. However, the process errors out… --- ## [RNA-Seq pipeline fails early](https://community.seqera.io/t/rna-seq-pipeline-fails-early/1239)
**Author:** [@Srividya\_Akella](https://community.seqera.io/u/Srividya_Akella)\ **Replies:** 4\ **Last updated:** [December 10, 2025, 3:27pm UTC](https://community.seqera.io/t/rna-seq-pipeline-fails-early/1239 "2025-12-10T15:27:46Z")
Hello all, I am attempting to run nf-core/rnaseq pipeline on GCP as a google batch job. Pipeline is running into an error quite early with nextflow.log indicating an issue possibly with the Trimgalore step or Google api … --- ## [New nf-core training materials released](https://community.seqera.io/t/new-nf-core-training-materials-released/2475)
**Author:** [@GeraldineVdA](https://community.seqera.io/u/GeraldineVdA)\ **Replies:** 0\ **Last updated:** [November 24, 2025, 3:47pm UTC](https://community.seqera.io/t/new-nf-core-training-materials-released/2475 "2025-11-24T15:47:56Z")
Happy Monday everyone! I wanted to let you know we just released version 2.8.0 of the training materials, featuring the completed Hello nf-core course. Please see the release notes link for more details. If you take thi… --- ## [Apply to become a Nextflow Ambassador in 2026!](https://community.seqera.io/t/apply-to-become-a-nextflow-ambassador-in-2026/2472)
**Author:** [@Lizzie\_Bolitho](https://community.seqera.io/u/Lizzie_Bolitho)\ **Replies:** 0\ **Last updated:** [November 24, 2025, 8:35am UTC](https://community.seqera.io/t/apply-to-become-a-nextflow-ambassador-in-2026/2472 "2025-11-24T08:35:13Z")
Ready to take your involvement with the Nextflow community to the next level? :up\_arrow: Apply to become a Nextflow Ambassador in 2026! :globe\_showing\_europe\_africa: Impact: Help grow the Nextflow and nf-core ecosystem… --- ## [Error Running a workflow](https://community.seqera.io/t/error-running-a-workflow/2463)
**Author:** [@Ashita2619](https://community.seqera.io/u/Ashita2619)\ **Replies:** 3\ **Last updated:** [November 21, 2025, 7:16pm UTC](https://community.seqera.io/t/error-running-a-workflow/2463 "2025-11-21T19:16:55Z")
.nextflow.log (7.5 KB) I am running an open source workflow GitHub - CDCgov/mycosnp-nf: MycoSNP: Whol… --- ## [Missing required field on nf-core/sopa](https://community.seqera.io/t/missing-required-field-on-nf-core-sopa/2459)
**Author:** [@Jose\_Gracia](https://community.seqera.io/u/Jose_Gracia)\ **Replies:** 1\ **Last updated:** [November 21, 2025, 9:52am UTC](https://community.seqera.io/t/missing-required-field-on-nf-core-sopa/2459 "2025-11-21T09:52:20Z")
Hi everyone, I’m trying to run nf-core/sopa on my MACSima imaging samples. I’m working on a RedHat HPCC environment, using: Nextflow version: 25.10.0 nf-core/sopa revision: master (commit 11b4cccb7e) Container… [Next page](https://community.seqera.io/tag/nf-core/42.md?match_all_tags=true&page=1&tags%5B%5D=nf-core)