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Remove deprecated parameters from test profiles #840

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Merged
apeltzer merged 2 commits into from
Mar 17, 2022
Merged

Remove deprecated parameters from test profiles #840

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9377942
Remove deprecated parameters from test profiles
jfy133 Mar 10, 2022
68e92a9
Merge branch 'dev' into test-full-fix
jfy133 Mar 17, 2022
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -9,7 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Fixed`

- [#838] Fix --snpcapture_bed files not being picked up by Nextflow
- [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow
- Fix PMDtools reference mask not being picked up by Nextflow, and it's use being evaluated against --snpcapture_bed rather than --pmdtools_reference_mask

### `Dependencies`
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1 change: 0 additions & 1 deletion conf/test_full.config
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Expand Up @@ -21,7 +21,6 @@ params {
bwaalnl = 1024

run_bam_filtering = true
bam_discard_unmapped = true
bam_unmapped_type = 'discard'
bam_mapping_quality_threshold = 25

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1 change: 0 additions & 1 deletion conf/test_stresstest_human.config
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Expand Up @@ -24,7 +24,6 @@ params {
mtnucratio_header = 'ChrM'

run_bam_filtering = true
bam_discard_unmapped = true
bam_unmapped_type = 'discard'
bam_mapping_quality_threshold = 30

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