nf-core #rnasplice

Steven Wingett

01/27/2026, 5:25 PM

Hello everyone, Thanks to the nf-core community for putting together the rnasplice pipeline. I’ve just tried the pipeline but unfortunately after several hours it terminated with an error message. The error message is below. Does anybody have an idea what may have gone wrong (sorry for my ignorance, but I could not debug the issue myself.) I can provide further details if needed. Many thanks, Steven Run Name: angry_ptolemy
Execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 0.

The full error message was:

Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI (KO_180-WT_180)'

Caused by:

`Missing output file(s)

*.clustvec

expected by process `NFCORE_RNASPLICERNASPLICESUPPA_SALMON:CLUSTEREVENTS_IOI (KO_180-WT_180)``

Command executed:

suppa.py \

clusterEvents \

--dpsi KO_180-WT_180_transcript_diffsplice.dpsi \

--psivec KO_180-WT_180_transcript_diffsplice.psivec \

--dpsi-threshold 0.05 \

--eps 0.05 \

--metric euclidean \

--min-pts 20 \

--groups 1-3,4-6 \

--clustering DBSCAN \

-o KO_180-WT_180_transcript_cluster

cat -END_VERSIONS > versions.yml

"NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI":

suppa: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('suppa').version)")

END_VERSIONS

Command exit status:

Command output:

Number of clustered events: 114/624 (18.269231%)

Cluster 0 contains 71 events

Cluster 1 contains 43 events

The RMSSTD score for cluster 0 is 0.283342

The RMSSTD score for cluster 1 is 0.266318

The average silhouette score is : 0.755640

Command error:

INFO:   Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred

INFO:   Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred

INFO:   Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred

INFO:   Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred

Work dir:

/scratch/swingett/test_run_rnasplice/work/33/5d3fee492a0b37137d93458dc894f9

Container:

/public/singularity/containers/nextflow/depot.galaxyproject.org-singularity-suppa-2.3--py36_0.img

Tip: when you have fixed the problem you can continue the execution adding the option

-resume` to the run command line`

The command used to launch the workflow was as follows:

nextflow run nf-core/rnasplice -r 1.0.4 --input YB_RNA_datasheet.csv --contrasts YB_RNA_contrast.csv --genome homo_sapiens.GRCh38.release_102 -config /public/singularity/containers/nextflow/lmb-nextflow/lmb.config --outdir results_rnasplice -bg

Execution summary

Launch time

26-Jan-2026 10:22:33

Ending time

26-Jan-2026 19:49:47 (duration: 9h 27m 14s)

Total CPU-Hours

577.4 (0% failed)

Tasks stats

Succeeded: 88  Cached: 0  Ignored: 0  Failed: 4

Launch directory

/scratch/swingett/test_run_rnasplice

Work directory

/scratch/swingett/test_run_rnasplice/work

Project directory

/lmb/home/swingett/.nextflow/assets/nf-core/rnasplice

Script name

<http://main.nf|main.nf>

Script ID

93d808d3e7ec52e0026e14613cc4d4c9

Workflow session

f077060d-c424-428a-bd16-3043f97b0147

Workflow repo

<https://github.com/nf-core/rnasplice>

Workflow revision

1.0.4 (1d0494ae3402d1a46e0adadad24f81a0ff855c77)

Workflow profile

standard

Workflow container

Container engine

singularity

Wave enabled

false

Fusion enabled

false, version -

Nextflow version

25.10.3, build 10983 (22-01-2026 15:34 UTC)

Maria Kondili

04/15/2026, 2:17 PM

Hello dear nf-core community ! I would like some help and suggestions on why the TEST of nf-core/rnasplice would give this error on clustering from SUPPA-module:

task: name=NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOE (YRI-GBR); work-dir=/shared/ifbstor1/projects/EPIS_SAV/NF_Core_rnasplice/work/b4/c14bf30ed590b999d1bbc709db90b3

`error [nextflow.exception.MissingFileException]: Missing output file(s)

*.clustvec

expected by process `NFCORE_RNASPLICERNASPLICESUPPA_SALMON:CLUSTEREVENTS_IOE (YRI-GBR)``

Mar-27 15:43:32.298 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for

task: name=NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI (GBR-YRI); work-dir=/shared/ifbstor1/projects/EPIS_SAV/NF_Core_rnasplice/work/f5/164864610611480584d75053e7ecb5

`error [nextflow.exception.MissingFileException]: Missing output file(s) `.clustvec`* expected by process `NFCORE_RNASPLICERNASPLICESUPPA_SALMON:CLUSTEREVENTS_IOI (GBR-YRI)``

Mar-27 15:43:34.086 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for

task: name=NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI (YRI-GBR); work-dir=/shared/ifbstor1/projects/EPIS_SAV/NF_Core_rnasplice/work/ab/c11527f40c487eda8e8c8fea079629

From the .nextflow.log we can read:

-[nf-core/rnasplice] Pipeline completed with errors-

ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOE (GBR-YRI)'

Caused by:

`Missing output file(s)

*.clustvec

expected by process `NFCORE_RNASPLICERNASPLICESUPPA_SALMON:CLUSTEREVENTS_IOE (GBR-YRI)``

Command executed:

suppa.py \

clusterEvents \

--dpsi GBR-YRI_local_diffsplice.dpsi \

--psivec GBR-YRI_local_diffsplice.psivec \

--dpsi-threshold 0.05 \

--eps 0.05 \

--metric euclidean \

--min-pts 20 \

--groups 1-2,3-4 \

--clustering DBSCAN \

-o GBR-YRI_local_cluster

Command output:

Number of clustered events: 0/6 (0.000000%)

Impossible to calculate silhouette score. Only 1 cluster group identified.

The command I run is :

nextflow run nf-core/rnasplice -r 1.0.4 -profile test,ifb_core --outdir ${out_dir}

piplus2

05/19/2026, 10:06 AM

Hi, is there anyone working on the compatibility with nextflow 26+? I've seen that CI are broken at the moment as they use the latest version of nextflow.

Uri David Akavia

06/18/2026, 1:37 PM

Hi. I'm working on making rmats nf-core compatible. I've done rmats prep, and I'm working on post. I'd like to put the rmats output in nf-core/testdatasets, so I can test each step (rmats prep, rmats post, rmats stats). So, I'm going to upload the rmats prep output. Would you prefer 1. I make a pull request to rnasplice branch on nf-core/testdatasets? 2. Make a pull request and upload to nf-core/modules branch? Thank you

Yann Vanrobaeys

10/02/2026, 7:56 PM

Following up on @piplus2 message, still no fix for compatibility with nextflow 26+?

piplus2

10/02/2026, 8:06 PM

Hi @Yann Vanrobaeys , I'm currently maintaining the pipeline. The dev version works with 26+

✅ 1

Full test notifications

10/09/2026, 5:26 PM

❌ rnasplice/test_full failed 😿 Run Name sick_descartes Duration 1.5s Status ❌ Failed Error Message

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Script compilation error
- file : /.nextflow/assets/.repos/nf-core/rnasplice/clones/358d6c745914270c1b9562363f23a0c11a4dd9e6/main.nf
- cause: Unexpected input: '{' @ line 12, column 8.
   params {
          ^

1 error

NOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced.

Command Line

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nextflow run '<https://github.com/nf-core/rnasplice>' -name sick_descartes -params-file '<https://api.cloud.seqera.io/ephemeral/b5vSLExK1TCuO6F_m7Aufg.json>' -with-tower -r 358d6c745914270c1b9562363f23a0c11a4dd9e6 -profile test_full

Oct 9, 2026 at 5:26 PM

Full test notifications

10/10/2026, 8:15 AM

❌ rnasplice/test_full failed 😿 Run Name irreverent_poincare Duration 1.5s Status ❌ Failed Error Message

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Script compilation error
- file : /.nextflow/assets/.repos/nf-core/rnasplice/clones/7dc005c7d2fb8436596f0919d3568a4fccaed6f9/main.nf
- cause: Unexpected input: '{' @ line 12, column 8.
   params {
          ^

1 error

NOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced.

Command Line

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nextflow run '<https://github.com/nf-core/rnasplice>' -name irreverent_poincare -params-file '<https://api.cloud.seqera.io/ephemeral/EZecAN3zMX7VcyEIi3AKPA.json>' -with-tower -r 7dc005c7d2fb8436596f0919d3568a4fccaed6f9 -profile test_full

Oct 10, 2026 at 8:15 AM

Full test notifications

10/10/2026, 11:53 AM

❌ rnasplice/test_full failed 😿 Run Name crazy_ardinghelli Duration 27.6s Status ❌ Failed Error Message

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Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/rnasplice>, projectDir: /.nextflow/assets/.repos/nf-core/rnasplice/clones/bfa5aa043c60a1ec1d515306f958e39b0fc11fd2, commitId: bfa5aa043c60a1ec1d515306f958e39b0fc11fd2, revision: null, startTime: 2026-10-10T11:52:50.716082839Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/rnasplice>' -name crazy_ardinghelli -params-file '<https://api.cloud.seqera.io/ephemeral/kSF8hg9m702f194s_d5ASg.json>' -with-tower -r bfa5aa043c60a1ec1d515306f958e39b0fc11fd2 -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.0, build:12031, timestamp:29-04-2026 04:00 UTC, preview:nextflow.NextflowMeta$Preview@7bbec1cc, enable:nextflow.NextflowMeta$Features@5a77b7cc, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/rnasplice/work-bfa5aa043c60a1ec1d515306f958e39b0fc11fd2, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

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nextflow run '<https://github.com/nf-core/rnasplice>' -name crazy_ardinghelli -params-file '<https://api.cloud.seqera.io/ephemeral/kSF8hg9m702f194s_d5ASg.json>' -with-tower -r bfa5aa043c60a1ec1d515306f958e39b0fc11fd2 -profile test_full

Oct 10, 2026 at 11:53 AM

Thomas Weber

10/13/2026, 9:25 PM

depictio Depictio dashboard for rnasplice: your feedback wanted Hi all! 👋 I am building Depictio, an open-source platform from EMBL to explore pipeline results without writing a Shiny or Streamlit app each time. A pipeline gets a dashboard template: a short definition that turns the outputs of any run into an interactive dashboard. I am now sharing it more widely, so I would like the view of rnasplice users and developers. ✨ What it does • MultiQC reports (aggregated across runs) next to result tables, images, phylogenetic trees, maps... with linked filters • Reusable: point the template at any new run of the same pipeline and you get the same dashboard • Fully editable: modify any dashboard from the GUI or in YAML, so the template is a starting point, not a constraint • Versioned, with comments and annotations on any component • Runs as a Python package, with Docker Compose or on Kubernetes, and can serve as a companion web app for a publication 🔀 For rnasplice: sample PCA, which genes each tool calls and where the tools agree, DEXSeq and edgeR exon usage, DEXSeq transcript usage, and rMATS and SUPPA2 splicing events, next to the MultiQC report. ⚖️ Compared with shinyngs: for the differential expression part, the usual route is nf-core/differentialabundance, which builds an R/Shiny app (shinyngs) from a matrix and a design. Depictio is not tied to R or to one data type: it shows the same kind of results (PCA, volcano, MA, GSEA) next to the MultiQC report and the other outputs of the run, behind one link, with versioning and comments. I see it as complementary: shinyngs is made for exploring expression data, Depictio for sharing the whole run. 👀 What I need: I have built 25 templates and want people who really use these pipelines to review and criticise them. What is useful? What is misleading? 👉 Dashboard: rnasplice dashboard (no account needed) 💬 Comment on the dashboard (Google sign-in) or in the GitHub discussion dedicated to rnasplice. ⭐ A star on the repo is welcome if you find it useful. Thanks! 🙏 🎤 In you're interested in the project, I was speaking about Depictio at the Nextflow Summit (session page), and the recording will be available in the coming weeks.

🎉 1

piplus2

10/14/2026, 6:31 AM

Hi @Thomas Weber, thanks for this! It's a great project. I'll definitely include in my daily work 🚀

depictio 1

Full test notifications

10/15/2026, 9:50 PM

✅ rnasplice/test_full completed successfully! 🎉 Run Name furious_chandrasekhar Duration 5h 59m 51s Status ✅ Success Tasks Completed: 166 Oct 15, 2026 at 9:50 PM

Full test notifications

10/20/2026, 11:38 AM

❌ rnasplice/test_full failed 😿 Run Name gloomy_lichterman Duration 1h 50m 15s Status ❌ Failed Error Message

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java.nio.file.NoSuchFileException: the path: <s3://nf-core-awsmegatests/rnasplice/results-dev/misopy/index/chr10/ENSG00000238552.pickle> does not exist

Command Line

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nextflow run '<https://github.com/nf-core/rnasplice>' -name gloomy_lichterman -params-file '<https://api.cloud.seqera.io/ephemeral/pt0qUo15ot7U_WxUFb429g.json>' -with-tower -r dev -profile test_full

Oct 20, 2026 at 11:38 AM

Full test notifications

10/20/2026, 12:21 PM

❌ rnasplice/test_full failed 😿 Run Name ridiculous_becquerel Duration 2h 10m 21s Status ❌ Failed Error Message

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java.nio.file.FileAlreadyExistsException: target already exists: <s3://nf-core-awsmegatests/rnasplice/results-dev/misopy/index/chr12/ENSG00000002016.pickle>

Command Line

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nextflow run '<https://github.com/nf-core/rnasplice>' -name ridiculous_becquerel -params-file '<https://api.cloud.seqera.io/ephemeral/LGd9-cgPVa92bclUAoqvuw.json>' -with-tower -r dev -profile test_full

Oct 20, 2026 at 12:21 PM

Full test notifications

10/20/2026, 1:40 PM

✅ rnasplice/test_full completed successfully! 🎉 Run Name hungry_coulomb Duration 4h 51m 54s Status ✅ Success Tasks Completed: 166 Oct 20, 2026 at 1:40 PM

piplus2

10/20/2026, 3:30 PM

🎉 nf-core/rnasplice 2.0.0 "Fenix Reborn" is out! phoenix After a long break since 1.0.4, rnasplice is back: a fresh template, LeafCutter, IsoformSwitchAnalyzeR and tests everywhere. Release notes: github.com/nf-core/rnasplice/…/2.0.0 Thanks to @Simon Pearce for supporting my involvement in the development of the pipeline! Huge thanks to everyone who helped along the way 🙏 • @Daniel Lundin and @mashehu for reviewing pretty much everything and making it so much better • @lathika, @Jesse Angelis, @Lorena Pantano, @Alexandra Bartlett, @felix.haidle615, @fhausmann471, @Tim Fallon, @Adam Talbot and @James Ashmore for the code • @Alba Mas Malavila, @Oliverfudj, @mlbonatelli, @misiti-1864309 and @srira25 for the bug reports and ideas • and all the other reviewers who chipped in! Keep the issues and ideas coming 😊 Some @ handles are GitHub usernames as I couldn't find them on Slack.

🙌 4

Full test notifications

10/20/2026, 3:45 PM

✅ rnasplice/test_full completed successfully! 🎉 Run Name admiring_caravaggio Duration 5h 31m 46s Status ✅ Success Tasks Completed: 166, Failed: 1 Oct 20, 2026 at 3:45 PM

🙌 1

piplus2

10/22/2026, 3:22 PM

New feature added to the

dev

version: input strandedness can be auto detected using rseqc and salmon by setting auto in the sample sheet. https://nf-co.re/rnasplice/dev/docs/usage/#strandedness

❤️ 1

🙏 1

piplus2

10/23/2026, 11:48 AM

`dev`: test data size has been reduced significantly to improve storage occupation and CI test runtime.

Roberto Aponte Rivera

10/26/2026, 3:02 AM

Consider adding the exon-based ASpli which produces both PSI and PIR results (bioconductor.org/packages/…/ASpli.html).

piplus2

10/26/2026, 6:35 AM

We'll do, thanks!

felix.haidle615

10/27/2026, 10:27 AM

Hi everyone! I'm planning to integrate two additional tools into rnasplice: IRFinder-S and MAJIQ. I've already implemented both in my own Nextflow pipeline, but I'd appreciate some guidance on how best to turn these into nf-core modules, particularly regarding dependencies and CI testing. Both tools come with a few challenges: IRFinder-S: • Not available on Conda, but the developers provide a working public Docker image. • Has a hardcoded minimum RAM requirement of 32 GB, which prevents it from running on standard GitHub Actions runners. MAJIQ: • Not available on Conda, and there is no official public container image. • Can be installed from its GitHub repository. In my current implementation, I build a custom Docker image in CI before running the pipeline. • Requires a license, which I currently handle using Nextflow secrets. Both tools are already working in my pipeline, which you can find here: github.com/ZarnackGroup/majiq_splicing_analysis_pipeline/tree/main I'm mainly wondering what the recommended nf-core approach would be for creating modules for these tools and handling their CI tests, given these limitations. Any advice on how best to proceed would be much appreciated!

piplus2

10/27/2026, 10:28 AM

Hi Felix, thanks for the message! One thing about MAJIQ. Doesn't it have a commercial license?

felix.haidle615

10/27/2026, 10:30 AM

it also has an academic license. majiq.biociphers.org/app_download

piplus2

10/27/2026, 10:32 AM

That gets linked to the person who fills the form, so it's tricky for the deployment. I'd say that it doesn't fit the licensing scheme of nf-core

piplus2

10/27/2026, 10:40 AM

IRFinder-S: that's tricky without conda because we need to cover also that in all pipelines. So one option is to create one and maintain it. Would you like to do that?

piplus2

10/27/2026, 10:47 AM

What about bioconductor.org/packages/…/ASpli.html as suggested by @Roberto Aponte Rivera?

piplus2

10/27/2026, 11:31 AM

I'm working on the implementation of ASpli

piplus2

10/28/2026, 12:52 PM

Added ASpli to

dev

. Now it can be triggered using the argument

--aspli

piplus2

10/29/2026, 5:26 PM

Thanks @Jonas S, that's great!

salute 1