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Update all nf-core modules (#139)
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* Update bcftools annotate

* Update bcftools concat

* Update bcftools convert

* Update bcftools index

* Update bcftools merge

* Update bcftools mpileup

* Update bcftools norm

* Update bcftools pluginsplit

* Update bcftools stats

* Update bcftools view

* Update bedtools makewindows

* Remove dumpsoftware

* Update gawk

* Update glimpse

* Update glimpse2

* Update gunzip

* Update quilt

* Update samtools

* Update shapeit5

* Update shapeit5

* Update stitch

* Update tabix

* Update vcflib

* Fix linting

* Update pluginsplit
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@LouisLeNezet
LouisLeNezet authored Oct 28, 2024
1 parent a4f6618 commit 8fb7bf0
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1 change: 1 addition & 0 deletions CHANGELOG.md
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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": {
"branch": "master",
"git_sha": "c1a7fa1c038061b344f2a41be71942061ec40d2e",
"git_sha": "cb08035150685b11d890d90c9534d4f16869eaec",
"installed_by": ["modules"],
"patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
},
"bcftools/concat": {
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"git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988",
"git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
"installed_by": ["modules"],
"patch": "modules/nf-core/bcftools/concat/bcftools-concat.diff"
},
"bcftools/convert": {
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"git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bcftools/index": {
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"git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["bam_impute_glimpse", "vcf_phase_shapeit5"]
},
"bcftools/merge": {
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"patch": "modules/nf-core/bcftools/merge/bcftools-merge.diff"
},
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"patch": "modules/nf-core/bcftools/mpileup/bcftools-mpileup.diff"
},
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"bcftools/stats": {
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"patch": "modules/nf-core/gawk/gawk.diff"
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"glimpse/chunk": {
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"installed_by": ["bam_impute_glimpse"]
},
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},
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"installed_by": ["bam_impute_glimpse"]
},
"glimpse2/chunk": {
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"git_sha": "cc64e71652f67ce627064af51008fe0a00850987",
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"patch": "modules/nf-core/glimpse2/chunk/glimpse2-chunk.diff"
},
"glimpse2/concordance": {
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},
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},
"glimpse2/phase": {
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"patch": "modules/nf-core/glimpse2/phase/glimpse2-phase.diff"
},
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"gunzip": {
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},
"multiqc": {
Expand All @@ -130,80 +125,80 @@
},
"quilt/quilt": {
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"stitch": {
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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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