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Release PR v1.8.0 #199

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merged 57 commits into from
Sep 24, 2024
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0ecfcab
bump to 1.8.0dev
nvnieuwk Aug 23, 2024
0754de2
first batch of updates
nvnieuwk Aug 28, 2024
fe7cfad
second batch of updates
nvnieuwk Aug 28, 2024
b96e082
third batch of updates
nvnieuwk Aug 28, 2024
a4581f2
fourth batch of updates
nvnieuwk Aug 28, 2024
fcb0d19
update configs
nvnieuwk Aug 29, 2024
70e8c24
update changelog
nvnieuwk Aug 29, 2024
d46f82d
update config includes
nvnieuwk Aug 29, 2024
a35e9c2
use nf-core dev for linting
nvnieuwk Aug 29, 2024
a06b09a
bump minimal nextflow version
nvnieuwk Aug 29, 2024
ee0b537
remove whitespace
nvnieuwk Aug 29, 2024
aaf2d7a
Merge pull request #188 from nf-cmgg/ben-made-me-do-this
nvnieuwk Aug 29, 2024
42ff0b1
first steps
nvnieuwk Sep 3, 2024
58e75ef
resolve all non module linting issues
nvnieuwk Sep 3, 2024
e94291f
update all modules
nvnieuwk Sep 4, 2024
6d2cdd4
pre-commit
nvnieuwk Sep 4, 2024
212370b
prettier
nvnieuwk Sep 4, 2024
0a81d13
fix validate tests
nvnieuwk Sep 4, 2024
5b49b84
fix somalier tests
nvnieuwk Sep 5, 2024
e33f082
fix somalier tests
nvnieuwk Sep 5, 2024
f852ed2
fix rtgtools testz
nvnieuwk Sep 5, 2024
b481cb5
fix rtgtools testz
nvnieuwk Sep 5, 2024
20411ca
fix more failing tests
nvnieuwk Sep 5, 2024
2adfe1b
fix all the things?
nvnieuwk Sep 5, 2024
9630006
update changelog
nvnieuwk Sep 5, 2024
1565a9f
fix final test?
nvnieuwk Sep 5, 2024
e668130
make nf-core happy again
nvnieuwk Sep 5, 2024
9a0b314
implement watchpath
nvnieuwk Sep 5, 2024
722e4eb
fix some more issues found with the new import
nvnieuwk Sep 6, 2024
6c88b6f
Fix haplotyper resource usage (#192)
matthdsm Sep 10, 2024
2fc05a5
reintroduce nf-core lint support + update all modules (#190)
nvnieuwk Sep 10, 2024
0a9c6b8
nf-core modules update (#193)
matthdsm Sep 10, 2024
a27874b
set igenomes ignore to true by default
matthdsm Sep 10, 2024
3726a04
fix tests
nvnieuwk Sep 20, 2024
cc20971
Merge branch 'watchpath-support' of https://github.com/nf-cmgg/germli…
nvnieuwk Sep 20, 2024
0e99623
fix some small issues
nvnieuwk Sep 20, 2024
6f687b9
fix unresolved merge conflicts
nvnieuwk Sep 20, 2024
bb46fe2
make pre-commit happy
nvnieuwk Sep 20, 2024
963f6b5
[no-cancel] fix nf-core lint
nvnieuwk Sep 20, 2024
4efe0e3
[no-cancel] fix nf-core lint
nvnieuwk Sep 20, 2024
773eeaf
fix prepare tests
nvnieuwk Sep 23, 2024
c9c4134
undo no cancel
nvnieuwk Sep 23, 2024
3c5cf09
fix snapshots
nvnieuwk Sep 23, 2024
56ba4a1
make genomes ignore true
nvnieuwk Sep 23, 2024
070a9cb
fix an issue with the validation workflow
nvnieuwk Sep 23, 2024
7fc0208
Merge pull request #196 from nf-cmgg/watchpath-support
nvnieuwk Sep 23, 2024
fd15c14
also filter out low coverage regions
nvnieuwk Sep 23, 2024
9ac108f
update changelog
nvnieuwk Sep 23, 2024
df9ecc3
fix snap
nvnieuwk Sep 23, 2024
906cc8a
Merge pull request #197 from nf-cmgg/callable-regions
nvnieuwk Sep 23, 2024
231059a
rename master branch to main
nvnieuwk Sep 23, 2024
43b732c
Merge branch 'dev' into rename-master-to-main
nvnieuwk Sep 23, 2024
f6ac2f7
fix nf-core lint
nvnieuwk Sep 23, 2024
6f58734
Merge branch 'rename-master-to-main' of https://github.com/nf-cmgg/ge…
nvnieuwk Sep 23, 2024
9106381
Merge pull request #198 from nf-cmgg/rename-master-to-main
nvnieuwk Sep 23, 2024
780e3fa
Merge branch 'dev' of https://github.com/nf-cmgg/germline into dev
nvnieuwk Sep 23, 2024
2556e9c
update version
nvnieuwk Sep 23, 2024
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update config includes
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nvnieuwk committed Aug 29, 2024
commit d46f82d8412c9253a57665683e268f3bb0e00f57
7 changes: 3 additions & 4 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -113,10 +113,10 @@ params {
includeConfig 'conf/base.config'

// Load nf-core custom profiles from different Institutions
includeConfig { !System.getenv('NXF_OFFLINE') ? "${params.custom_config_base}/nfcore_custom.config" : "conf/empty.config" }
includeConfig !System.getenv('NXF_OFFLINE') ? "${params.custom_config_base}/nfcore_custom.config" : "conf/empty.config"

// Include test data config
includeConfig { !System.getenv('NXF_OFFLINE') ? 'https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/nf-cmgg-testdata.config' : "conf/empty.config" }
includeConfig !System.getenv('NXF_OFFLINE') ? 'https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/nf-cmgg-testdata.config' : "conf/empty.config"

profiles {
debug {
Expand All @@ -132,7 +132,6 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
Expand Down Expand Up @@ -253,7 +252,7 @@ validation {
}
}

includeConfig { !params.igenomes_ignore ? "conf/igenomes.config" : !params.genomes_ignore ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" : "conf/empty_genomes.config" }
includeConfig !params.igenomes_ignore ? "conf/igenomes.config" : !params.genomes_ignore ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" : "conf/empty_genomes.config"

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
Expand Down
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