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Fix intermediate files published #681

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merged 4 commits into from
Jul 22, 2022
Merged

Fix intermediate files published #681

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887de62
disable publish from FREEBAYES process
maxulysse Jul 22, 2022
598a005
update expected output from tests
maxulysse Jul 22, 2022
d78b331
Merge remote-tracking branch 'upstream/dev' into dev_freebayes
maxulysse Jul 22, 2022
910440f
update CHANGELOG
maxulysse Jul 22, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed

- [#679](https://github.com/nf-core/sarek/pull/679) - Fixed typos in subway maps
- [#681](https://github.com/nf-core/sarek/pull/681) - Fixed intermediate files published cf [#680](https://github.com/nf-core/sarek/issues/680)

### Deprecated

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3 changes: 3 additions & 0 deletions conf/modules.config
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Expand Up @@ -607,6 +607,9 @@ process{
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" }
ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1'
ext.when = { params.tools && params.tools.split(',').contains('freebayes') }
publishDir = [
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why is this happening though? shouldn't publishing be disabled by default?

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I agree but it was

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I believe you :D just wondering if something else is going on somewhere.

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I'm sure something else is going on. I'll check it more more in detail next week

enabled: false
]
}

withName: 'BCFTOOLS_SORT' {
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