A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Getting an nf-test error after template merge when attempting to update the snapshots in gh codespaces (thread)

```/workspaces/epitopeprediction -&gt; nf-test test tests/ --profile=+singularity --update-snapshot

🚀 nf-test 0.9.3
<https://www.nf-test.com>
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar
Warning: every snapshot that fails during this test run is re-recorded.

Test pipeline

  Test [7f0ec3f9] '-profile test' Assertion failed: 

assert workflow.success
       |        |
       workflow false

Error reading YAML file: /workspaces/epitopeprediction/.nf-test/tests/7f0ec3f9fd43f76b5becf116d3b39c42/output/pipeline_info/nf_core_epitopeprediction_software_mqc_versions.yml (No such file or directory)
FAILED (2.59s)

  Assertion failed: 
  
  1 of 2 assertions failed
  
  Nextflow stdout:
  
  ERROR ~ Unknown method invocation `startsWith` on ConfigObject type
  
   -- Check '/workspaces/epitopeprediction/.nf-test/tests/7f0ec3f9fd43f76b5becf116d3b39c42/meta/nextflow.log' file for details
  Nextflow stderr:```
The conflicting line is
```//aws.client.anonymous = !params.igenomes_ignore &amp;&amp; params.igenomes_base?.startsWith('<s3://ngi-igenomes/igenomes/>') ?: false```
in the `nextflow.config` . Commenting it out (I don’t need) solves the issue

Not sure where to put it, but I wanted to share that one

```lint:
  files_unchanged:
    - assets/nf-core-epitopeprediction_logo_light.png
    - docs/images/nf-core-epitopeprediction_logo_light.png
    - docs/images/nf-core-epitopeprediction_logo_dark.png
nf_core_version: 3.4.1
repository_type: pipeline
template:
  author: Christopher Mohr, Jonas Scheid
  description: A fully reproducible and state of the art epitope prediction pipeline.
  force: false
  is_nfcore: true
  name: epitopeprediction
  org: nf-core
  outdir: .
  version: 2.3.1```

I get the same error with <#CE9BJ6X6V|> with this yml
```lint:
  files_unchanged:
    - .github/CONTRIBUTING.md
    - .vscode/settings.json
nf_core_version: 3.4.1
repository_type: pipeline
template:
  author: Jonas Scheid, Steffen Lemke, Leon Bichmann, Marissa Dubbelaar
  description: Identify and quantify peptides from mass spectrometry raw data
  force: false
  is_nfcore: true
  name: mhcquant
  org: nf-core
  outdir: .
  version: 3.1.0```

ah, you are not using igenomes, so you should add it to the `skip_features` in there for the future. this is a new igenomes params entry and requires previously added igenome parameters, that you removed in a previous commit probably.