# Fusion v2 Compatibility Report — nf-core Pipelines

Updated: 2026-03-11
Source: nf-core megatest runs on [Seqera Platform](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests)

## Methodology

Of the [91 released nf-core pipelines](https://nf-co.re/pipelines), full-size tests (`test_full` profile) were run on AWS Batch via Seqera Platform. Fusion status was verified by checking `fusion.enabled = true` in the resolved Nextflow config for each run. For older runs where the compute environment has since been deleted, fusion was confirmed via `/fusion/s3/` workdir paths where possible. Runs were executed between late 2025 and February 2026, with the majority re-run in the February 2026 megatest batch using Nextflow 25.10.2 on the `aws_ireland_fusionv2_nvme_cpu_snapshots` compute environment.

## Summary

| Category | Count |
|----------|------:|
| PASS with fusion enabled | 50 |
| PASS on non-fusion CE (PlainS3 queue) | 3 |
| FAIL — fusion-related | 6 |
| FAIL — not fusion-related | 16 |
| No full-size test run | 16 |
| **Total** | **91** |

Of the 53 pipelines with a successful full-size test, **50 (94%) ran with fusion enabled**. Only 3 pipelines required a non-fusion compute environment. Of the 6 fusion-related failures, all are tied to specific product-level limitations documented below.

## Confirmed fusion-compatible (50 pipelines)

These pipelines completed their full-size test with `fusion.enabled = true` (verified from resolved run config).

**Note on older runs**: 15 of these pipelines were tested on a fusion CE that has since been deleted. The CE can no longer be inspected, but fusion compatibility was confirmed via `/fusion/s3/` workdir paths and/or the resolved config at run time. These are marked with `*` below. Re-running these on the current CE would strengthen the evidence.

| Pipeline | Version | Run | Notes |
|----------|---------|-----|-------|
| atacseq | 2.1.2 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3o3z6qCs78Etek) | `*` Ran on older (now deleted) fusion CE |
| bamtofastq | 2.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/VUMiQY24Nve22) | Per-process workaround: `CHECK_IF_PAIRED_END` process routed to non-fusion EBS queue (1 task failed, pipeline overall SUCCEEDED) |
| chipseq | 2.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/NKFfx6SaV3KOm) | `*` Ran on older (now deleted) fusion CE |
| createtaxdb | 2.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4Xok1DfBJenYWa) | |
| cutandrun | 3.2.2 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4zNDjKfiObtmpS) | `*` Ran on older (now deleted) fusion CE |
| demo | 1.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1ZCnVyds7Gos5s) | |
| demultiplex | 1.7.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3dsDIgTmXmScJb) | |
| denovotranscript | 1.2.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3BMDeoThi4ewJv) | |
| detaxizer | 1.3.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5sAMJCAwCcx1Xu) | |
| differentialabundance | 1.5.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5yLmwyFcxbj1FO) | `*` Ran on older (now deleted) fusion CE |
| drugresponseeval | 1.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4Asci7EmH4hBpy) | |
| epitopeprediction | 3.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3xwRBsRpr4phU7) | |
| fastqrepair | 1.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/TKptyuCYu3On8) | |
| fastquorum | 1.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3LxlfvqWLLeAOe) | `*` Ran on older (now deleted) fusion CE |
| fetchngs | 1.12.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5jYjLDuoY0FhmL) | `*` Ran on older (now deleted) fusion CE |
| funcscan | 3.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/JGVXiwO7lDGzc) | |
| hic | 2.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5hMt24yKi5Qkyu) | `*` Ran on older (now deleted) fusion CE |
| hicar | 1.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1jblYjkNkefArA) | `*` Fusion confirmed via `/fusion/s3/` workdir path; ran on older (now deleted) CE |
| isoseq | 2.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/25q84xaIxy3H0d) | `*` Ran on older (now deleted) fusion CE |
| mag | 5.4.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/NfLKW4LHKPMYf) | `METASPADES` uses `scratch=true` (SPAdes needs local disk); 14 tasks failed via `errorStrategy 'ignore'` on non-critical processes (MAXBIN2, GTDBTK, etc.) |
| magmap | 1.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1tFjgfCjWOOCTv) | |
| marsseq | 1.0.3 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4RynKquUG7ssNS) | `*` Ran on older (now deleted) fusion CE |
| metaboigniter | 2.0.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1n5wpYDHvX9twE) | `*` Ran on older (now deleted) fusion CE |
| metapep | 1.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4ikt3GOFHiMDYc) | `*` Ran on older (now deleted) fusion CE |
| methylseq | 4.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3IoZ6CfCSplPQW) | |
| mhcquant | 3.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2CMUncHIfZ8wqR) | |
| molkart | 1.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1AW6t0ROJkJe65) | |
| multiplesequencealign | 1.1.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3Nf2b1dblaoLHi) | `*` Ran on older (now deleted) fusion CE |
| nanoseq | 3.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3gl5yW3lD7HiXe) | `*` Ran on older (now deleted) fusion CE |
| nanostring | 1.3.3 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/11zYO8pdbzpEav) | |
| oncoanalyser | 2.3.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2Lq6LphiIOyWQz) | |
| pairgenomealign | 2.2.2 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5XITXsmYlh6uUD) | |
| pangenome | 1.1.3 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3hqEPYgVjcWcpl) | |
| phaseimpute | 1.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/vFKzfCfQO99Py) | |
| phyloplace | 2.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3TrwqbQroP70Gv) | `*` Ran on older (now deleted) fusion CE |
| pixelator | 2.3.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/LMOE2D91gGHgw) | |
| proteinannotator | 1.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1ZNarfygldbxRs) | |
| proteinfamilies | 2.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3Szyijck6fVTv0) | |
| proteinfold | 1.1.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5bLuc56HKLmUX5) | `*` Ran on older (now deleted) fusion CE |
| quantms | 1.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2doR4aF0IB4mHY) | `*` Ran on older (now deleted) fusion CE |
| readsimulator | 1.0.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5atyRLZxKD82B1) | `*` Ran on older (now deleted) fusion CE |
| riboseq | 1.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5X7aE7eWd6q5y8) | |
| rnaseq | 3.23.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5WFOS0R5gVTzEq) | |
| rnavar | 1.2.3 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/49OrPIiD2eGtvh) | |
| sarek | 3.8.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4uhtxVmmO0e3DC) | Resumed run (237 cached / 24 succeeded) |
| seqinspector | 1.0.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4F2w20rGO4LQJ7) | |
| smrnaseq | 2.4.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/219TpksJBfHJd2) | |
| taxprofiler | 1.2.6 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5KqZKNYcfcBdXF) | |
| variantbenchmarking | 1.4.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4xN0acljOsXR7q) | |
| viralmetagenome | 1.1.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/25HVCz2aoWFhqI) | |

## Fusion-incompatible — known issues (6 pipelines)

These pipelines fail on the fusion CE due to fusion-specific limitations.

| Pipeline | Version | Issue | Severity |
|----------|---------|-------|----------|
| metatdenovo | 1.3.0 | `EGGNOG_DOWNLOAD` fails — downloading large databases via wget into fusion mount | High — pipeline fails |
| methylong | 2.0.0 | `Module file size cannot be bigger than 1 MB` — ccsmeth model in `bin/` exceeds fusion file size limit | High — pipeline cannot run with fusion |
| pathogensurveillance | 1.1.0 | `Unexpected path for Fusion script launcher: /path_surveil_data/busco_db` | High — pipeline fails |
| rnafusion | 4.0.0 | FusionReport tool needs EBS queue; still failing after workaround | High — pipeline fails |
| scnanoseq | 1.2.1 | `.command.sh: Argument list too long` — samtools call hits OS arg length limit, likely due to fusion path expansion. **Note**: 1.2.2 released 2026-03-09 (after this test); not yet re-tested. | High — pipeline fails |
| viralintegration | 0.1.1 | `STAR_ALIGN_HOST` fails on all samples (5/5 tasks failed) — STAR uses mmap which can conflict with FUSE mounts | High — pipeline fails |

### Issue categories for product

1. **Module file size limit (1 MB)**: Fusion rejects module files >1 MB. Any pipeline shipping large model files in `bin/` will hit this. Affects: methylong.

2. **Argument list too long**: Fusion path expansion can cause the OS argument length limit to be exceeded when a tool receives many input files. Affects: scnanoseq.

3. **Tool-specific I/O patterns**: Some tools assume local disk semantics that conflict with fusion's FUSE mount (e.g. FusionReport, STAR's mmap usage). Affects: rnafusion, viralintegration.

4. **Process-level incompatibility**: Specific processes that read from stdin or use features incompatible with fusion, but the rest of the pipeline works. Workaround: route affected process to a non-fusion queue. Affects: bamtofastq (listed under fusion-compatible with workaround).

5. **Large file downloads into fusion mount**: Tools that download large databases (multi-GB) directly into the fusion-mounted workdir can stall or fail. Affects: metatdenovo.

6. **Fusion script launcher path issues**: Fusion may reject certain filesystem paths used by pipelines. Affects: pathogensurveillance.

## Run on non-fusion CE (3 pipelines)

These pipelines passed their full-size test on a non-fusion compute environment (`aws_ireland_plains3_nvme_cpu_ebs_nofusion`). They have not been tested on a fusion CE.

| Pipeline | Version | Run | Notes |
|----------|---------|-----|-------|
| airrflow | 5.0.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5n2W3MYeP8dDhT) | No `fusion.enabled` in config; CE explicitly nofusion |
| ampliseq | 2.16.1 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/46ohSvQV8Uoo86) | QIIME2 processes need `scratch=true`; not attempted on fusion CE |
| hlatyping | 2.2.0 | [SUCCEEDED](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1Rdrvqxr13SLvo) | Entire pipeline incompatible with fusion; needs nofusion CE |

## FAIL — not fusion-related (16 pipelines)

These pipelines fail their full-size test regardless of whether fusion is enabled. The failures are due to pipeline bugs, missing/broken test inputs, DSL1 incompatibility, or infrastructure issues unrelated to fusion.

### Pipeline bugs — need maintainer action (8 pipelines)

| Pipeline | Version | Error | Runs |
|----------|---------|-------|------|
| coproid | 2.0.0 | NullPointerException | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3vwgQWHKFXb4jp) |
| crisprseq | 2.3.0 | Failing across 4 retries | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1eGSCqn0L8NwIu), [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2w3FCE1AnbQJ5T), [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5jg3GBazJ3VPyR), [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2uuonAhYHuFuvD) |
| genomeassembler | 1.1.0 | `toBoolean() on null object` | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1rmguQg2XDcXmL), [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/5BfZcl17POtit) |
| nascent | 2.3.0 | PINTS: "No signal found across all chromosomes" | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2qi4NbpJwBULCt) |
| rangeland | 1.0.0 | Unknown (2 retries) | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2bQ7bLUtX6ozHR), [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4qZMCjNc4WxZFi) |
| reportho | 1.1.0 | Unknown (2 retries) | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/22b0eGquneWWmj), [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1lcpfTRI75Yh85) |
| rnasplice | 1.0.4 | Missing output `*.clustvec` from `CLUSTEREVENTS_IOI` | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2aWwXr8uyvTeXe) |
| viralrecon | 3.0.0 | `UnboundLocalError: cannot access local variable 'pango_aliases'` | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/oXrKpGfptTodI) |

### Input / config / infra errors — need test_full fix (4 pipelines)

| Pipeline | Version | Error | Runs |
|----------|---------|-------|------|
| bacass | 2.5.0 | "Assembly type not provided" | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4JxnUjPL5BOSxa) |
| circdna | 1.1.0 | `--mosek_license_dir` expects directory, got file URL | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4vpMNAHudixzqN) |
| raredisease | 2.6.0 | Input validation: missing parameters | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/45IvPgXOfxKY1R) |
| scrnaseq | 4.1.0 | S3 Access Denied (403) | [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/28AIjsPbwhZIMa), [FAIL](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2UnHZHzzXM2zgz) |

### DSL1 — cannot run on current Nextflow (4 pipelines)

These pipelines are stuck on DSL1 and cannot run on Nextflow 25.x. They need a DSL2 migration or should be marked as archived.

| Pipeline | Version | Error |
|----------|---------|-------|
| callingcards | 1.0.0 | `No such property: WorkflowMain` (DSL1); Java major version 65 mismatch |
| eager | 2.5.3 | DSL1 + Java major version 65 mismatch |
| hgtseq | 1.1.0 | Can't parse config — DSL1 `params {}` syntax |
| mnaseseq | 1.0.0 | DSL1 pipeline |

## No full-size test run (16 pipelines)

### DSL1 — never launched (9 pipelines)

These were queued in the Feb 2026 rerun but seqerakit could not launch them because Nextflow 25.x cannot parse DSL1 configs.

cageseq (1.0.2), clipseq (1.0.0), diaproteomics (1.2.4), dualrnaseq (1.0.0), imcyto (1.0.0), kmermaid (0.1.0-alpha), proteogenomicsdb (1.0.0), proteomicslfq (1.0.0), slamseq (1.0.0)

### No runs found at all (5 pipelines)

| Pipeline | Version | Notes |
|----------|---------|-------|
| bactmap | 1.0.0 | No runs on platform |
| deepvariant | 1.0 | No runs on platform |
| hadge | 0.2.0 | No runs on platform |
| neutronstar | 1.0.0 | Legacy pipeline |
| references | 0.1 | Utility pipeline |

### Other (2 pipelines)

| Pipeline | Version | Notes |
|----------|---------|-------|
| longraredisease | v1.0.0-alpha | No first stable release |
| pacvar | 1.0.1 | Queued in Feb rerun but no matching run found on platform |