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Fix fusionreport download #386

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merged 5 commits into from
Aug 30, 2023
Merged

Fix fusionreport download #386

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0fbdfd1
fix fusionreport issue with MACOXS dir
rannick Aug 28, 2023
39390f1
update changelog
rannick Aug 28, 2023
ea8d9ec
update changelog
rannick Aug 30, 2023
bc10b08
Merge branch 'dev' into fix_fusionreport_download
rannick Aug 30, 2023
eb81ba0
Merge branch 'dev' into fix_fusionreport_download
rannick Aug 30, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379)
- Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380)
- Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385)
- Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386)

### Removed

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2 changes: 1 addition & 1 deletion modules/local/fusionreport/download/main.nf
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Expand Up @@ -4,7 +4,7 @@ process FUSIONREPORT_DOWNLOAD {

// Note: 2.7X indices incompatible with AWS iGenomes.
conda "bioconda::star=2.7.9a"
container "docker.io/clinicalgenomics/fusion-report:2.1.5p2.1"
container "docker.io/clinicalgenomics/fusion-report:2.1.5p3"
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what did you change in the container @rannick ? Also, did you test this works?

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Yes I tested the download of fusionreport references

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I modified this line: https://github.com/Clinical-Genomics/fusion-report/blob/e21f5f72eed0f1b80fd16d4741809fa0f3c7470a/fusion_report/common/net.py#L207
so that the files in the folder _MACOSX are not considered


input:
val(username)
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