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Bump netmhcpan version to 4.2#317

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jonasscheid merged 18 commits intodevfrom
update-netmhcpan
Jan 12, 2026
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Bump netmhcpan version to 4.2#317
jonasscheid merged 18 commits intodevfrom
update-netmhcpan

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@jonasscheid jonasscheid commented Dec 15, 2025 •
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/epitopeprediction branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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nf-core-bot commented Dec 15, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions Bot commented Dec 15, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 570887f

+| ✅ 256 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2026-01-09 09:31:00

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jonasscheid commented Dec 15, 2025

@copilot We currently dont have netmhcpan tests anymore. We did in the previous version via ci.yml (

epitopeprediction/.github/workflows/ci.yml

Line 120 in 37c08f0

nonfree:
). However the new ci tests are now running only via nf-test (https://github.com/nf-core/epitopeprediction/blob/dev/.github/actions/nf-test/action.yml) and we need to have netmhcpan 4.2 in there as well. Please parse the old ci logic into the new nf-test/action.yml

Copilot AI mentioned this pull request Dec 15, 2025
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Copilot AI commented Dec 15, 2025

@jonasscheid I've opened a new pull request, #318, to work on those changes. Once the pull request is ready, I'll request review from you.

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Add NetMHCpan 4.2 tests to nf-test workflow
a2e5137 
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
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jonasscheid commented Dec 31, 2025

@copilot update usage section in docs/usage.md such that users only use netMHCpan-4.2bstatic.Linux.tar.gz now. No other versions are supported, since we validate the correct tarball via the checksum. Same goes for netmhcIIpan4.3e

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Copilot AI commented Dec 31, 2025

@jonasscheid I've opened a new pull request, #322, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot AI mentioned this pull request Dec 31, 2025
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Copilot AI and others added 3 commits December 31, 2025 10:43
@jonasscheid
Update usage.md to specify only supported NetMHC versions
feac646 
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
@jonasscheid
Improve readability of NetMHC documentation
0e5d47e 
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
@jonasscheid
Merge pull request #322 from nf-core/copilot/sub-pr-317-again
7fafe60 
Update usage docs to specify NetMHC 4.2bstatic and NetMHCIIpan 4.3e as only supported versions
@jonasscheid jonasscheid changed the title bump to netmhcpan4.2 Bump netmhcpan version to 4.2 Dec 31, 2025
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jonasscheid commented Dec 31, 2025

@nf-core-bot fix linting

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Chiyun-Lee commented Jan 8, 2026

Hi @jonasscheid. Big fan of your work on this so far. Just wanted to mention that this new version also include different run modes:
-mode 0 # your usual one
-mode 1 # pathogen epitopes
-mode 2 # cancer epitopes

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jonasscheid commented Jan 8, 2026

Hi @Chiyun-Lee! That is great to know, thank you!

Do you know if the 2 other modes change the output columns of netmhcpan4.2? If not users could just provide their specific mode via an extra custom.config for netmhcpan like

epitopeprediction/conf/modules.config

Line 99 in 4c13c15

ext.args = "-BA"

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Update NetMHCpan download to use S3 bucket
fed10dc 
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
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Chiyun-Lee commented Jan 8, 2026

Here is an example of a mode 0 output:

Pos     Peptide ID      core    icore   Score   Rank    BA_score        BA_Rank Ave     NB
1       QLDIINKN        PEPLIST QLD-IINKN       QLDIINKN        0.000007        67.313835       0.007122        94.232468       0.000007             0
2       LYYGAYNK        PEPLIST LYY-GAYNK       LYYGAYNK        0.001972        12.067458       0.097358        13.646334       0.001972             0
3       IEEKICFD        PEPLIST IEEKI-CFD       IEEKICFD        0.000000        98.429497       0.010319        86.283730       0.000000             0

...and one of a mode 1 output:

Pos     Peptide ID      core    icore   Score   Rank    Ave     NB
1       QLDIINKN        PEPLIST QLD-IINKN       QLDIINKN        0.375298        64.453041       0.375298             0
2       LYYGAYNK        PEPLIST -LYYGAYNK       LYYGAYNK        0.554017        15.227778       0.554017             0
3       IEEKICFD        PEPLIST -IEEKICFD       IEEKICFD        0.217552        95.274666       0.217552             0

The BA_score and BA_Rank columns disappear when running on mode 1, it seems

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jonasscheid commented Jan 9, 2026

@Chiyun-Lee if you join the nf-core community on Github, you could give me a review on that PR :)

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jonasscheid commented Jan 9, 2026

@nf-core-bot fix linting

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Hi @jonasscheid this looks good, though I won't be able to run it on some actual data right now.

I think it might be worth considering whether you want to add some quality of life features around the different run modes. For a project I'm currently working on, I want the results of both mode 0 and mode 1 for each peptide, so I've hacked modules/local/netmhcpan/main.nf to literally run once on mode 0, then again on mode 1, and I then join the output .xls files before emitting in output. I'm in a bit of a rush so having to make-do with this.

It's also equally worth considering whether this is just a separate enhancement PR (and leave this PR to purely bump the netmhcpan version).

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jonasscheid commented Jan 12, 2026

It's also equally worth considering whether this is just a separate enhancement PR (and leave this PR to purely bump the netmhcpan version).

Going with this point. Technically you would also need to run netmhcpan 3x to get the output of all 3 modes right?

mashehu
mashehu approved these changes Jan 12, 2026
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Comment thread .github/workflows/nf-test.yml
Comment thread .github/workflows/nf-test.yml
Comment on lines +155 to +171
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: "${{ env.NFT_VER }}"
install-pdiff: true

- name: Run nf-test with NetMHCpan
continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
env:
NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
run: |
nf-test test \
--profile=+docker \
--tag netmhcpan \
--ci \
--verbose \
--tap=test.tap
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why not use the actions/nf-test action directly?

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Honestly, I do not fully understand how the tests are triggered and how I could change that. The complexitiy here is that for the netmhcpan test, we need a binary that needs to be downloaded from aws and unpacked. Then this unpacked folder needs to be present in the netmhcpan CI run to let tests run properly. If you have any suggestions how to improve this, I would be very happy to know!

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@mashehu Could you have a look at #328 if you have some time to spend? Trying to alter CI according to your input. Thank you!

Comment thread docs/usage.md
@jonasscheid jonasscheid merged commit ba00f34 into dev Jan 12, 2026
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jonasscheid commented Jan 12, 2026

Ah Sorry @mashehu, didn't see your comments on mobile. I'm gonna look into your points, thanks!

Copilot AI mentioned this pull request Jan 13, 2026
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Copilot AI added a commit that referenced this pull request Jan 13, 2026
@jonasscheid
Implement open comments from PR #317: use nf-test action and TMPDIR
e994985 
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
@jonasscheid jonasscheid deleted the update-netmhcpan branch March 4, 2026 10:30
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