Add nf-test for local module FUSIONINSPECTOR
#601
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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rannick
reviewed
Dec 27, 2024
| @@ -4,8 +4,8 @@ process FUSIONINSPECTOR { | |||
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| conda "${moduleDir}/environment.yml" | |||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |||
| 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' : | |||
| 'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}" | |||
| 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7d/7dbc3bb67499701633a925b0ed03f58ffb03d0a4c37a86a53c38ebe9a8a6cc37/data' : | |||
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This container does not seem to contain a fusioninspector executable
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Mmm, that's odd. I will run the nf-test again in singularity and check.
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The test did not fail for me but I made a few changes that could have been causing issues if you were trying to replicate it:
- Removed a hardcoded
starfusion_buildinvocation in the nf-test - Added a fixed version of
conda-forge::perl-carp-assert=0.21
Let me know if you are still encountering issues.
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This PR:
FUSIOINSPECTORto v2.10.0 and solves container not working in docker and singularity Fusioninspector singularity container not working #594PR checklist
nf-core lint).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).