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Update all nf-core modules #139

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merged 25 commits into from
Oct 28, 2024
Merged

Update all nf-core modules #139

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3873c15
Update bcftools annotate
LouisLeNezet Oct 28, 2024
8320188
Update bcftools concat
LouisLeNezet Oct 28, 2024
d4eef21
Update bcftools convert
LouisLeNezet Oct 28, 2024
8591d98
Update bcftools index
LouisLeNezet Oct 28, 2024
89a4c92
Update bcftools merge
LouisLeNezet Oct 28, 2024
5872546
Update bcftools mpileup
LouisLeNezet Oct 28, 2024
3aa60e9
Update bcftools norm
LouisLeNezet Oct 28, 2024
a89513d
Update bcftools pluginsplit
LouisLeNezet Oct 28, 2024
a772cac
Update bcftools stats
LouisLeNezet Oct 28, 2024
5d2a2d0
Update bcftools view
LouisLeNezet Oct 28, 2024
6cc74a8
Update bedtools makewindows
LouisLeNezet Oct 28, 2024
0c8b876
Remove dumpsoftware
LouisLeNezet Oct 28, 2024
ca22129
Update gawk
LouisLeNezet Oct 28, 2024
ca5f50e
Update glimpse
LouisLeNezet Oct 28, 2024
e321e4f
Update glimpse2
LouisLeNezet Oct 28, 2024
0f125bc
Update gunzip
LouisLeNezet Oct 28, 2024
1071bd6
Update quilt
LouisLeNezet Oct 28, 2024
2c30110
Update samtools
LouisLeNezet Oct 28, 2024
49d8960
Update shapeit5
LouisLeNezet Oct 28, 2024
039f485
Update shapeit5
LouisLeNezet Oct 28, 2024
c8b00df
Update stitch
LouisLeNezet Oct 28, 2024
d0f2d81
Update tabix
LouisLeNezet Oct 28, 2024
0a35afc
Update vcflib
LouisLeNezet Oct 28, 2024
28e0ff7
Fix linting
LouisLeNezet Oct 28, 2024
3ac3950
Update pluginsplit
LouisLeNezet Oct 28, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
- [#102](https://github.com/nf-core/phaseimpute/pull/102) - Update all test and recompute snapshot to match new version of the phaseimpute test dataset.
- [#103](https://github.com/nf-core/phaseimpute/pull/103) - Update Glimpse2 phase, gunzip and multiqc
- [#135](https://github.com/nf-core/phaseimpute/pull/135) - Impute by batch of 100 individuals by default using `--batch_size` parameter. All individuals BAM files are gathered and VCF are allowed for glimpse1 and glimpse2. Channel preprocessing of stitch is done in stitch subworkflow. Genotype likelihood computation for glimpse1 is now done outside of the subworkflow and merge the resulting vcf with all the samples. New test added to check batch separation. Improve `usage.md` documentation. Add validation to initialisation of the pipeline to ensure compatibility between tools, steps and the files provided by the user.
- [#139](https://github.com/nf-core/phaseimpute/pull/139) - Update all nf-core modules

### `Fixed`

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75 changes: 35 additions & 40 deletions modules.json
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Expand Up @@ -7,120 +7,115 @@
"nf-core": {
"bcftools/annotate": {
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"git_sha": "c1a7fa1c038061b344f2a41be71942061ec40d2e",
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"patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
},
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"installed_by": ["modules"],
"patch": "modules/nf-core/bcftools/concat/bcftools-concat.diff"
},
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"git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
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},
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},
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"multiqc": {
Expand All @@ -130,80 +125,80 @@
},
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"stitch": {
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"vcflib/vcffixup": {
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}
}
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21 changes: 15 additions & 6 deletions modules/nf-core/bcftools/annotate/bcftools-annotate.diff
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2 changes: 0 additions & 2 deletions modules/nf-core/bcftools/annotate/environment.yml
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10 changes: 5 additions & 5 deletions modules/nf-core/bcftools/annotate/main.nf
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