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Merge pull request #187 from LouisLeNezet/update
Update all modules
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‎CHANGELOG.md

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- [#175](https://github.com/nf-core/phaseimpute/pull/175) - Update TEMPLATE to nf-core tools version 3.2.0. Move `CHRCHECK` functions to the workflow directory.
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- [#182](https://github.com/nf-core/phaseimpute/pull/182) - Add dark version of the metromap and dynamically change it in the README.
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- [#185](https://github.com/nf-core/phaseimpute/pull/185) - Add `--sampleNames_file` option for `STICH` and `QUILT`.
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- [#187](https://github.com/nf-core/phaseimpute/pull/187) - Update modules and subworkflows
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### `Fixed`
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- [#185](https://github.com/nf-core/phaseimpute/pull/185) - Fix CSV generation and check that all mentioned path files exist.
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- [#189](https://github.com/nf-core/phaseimpute/pull/189) - Set meta map id as string to avoid error when using numbers in csv files.
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### `Dependencies`
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `gunzip` | 1.10 | 1.13 |
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| `lbzip2` | | 2.5 |
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| `shapeit5` | 1.0.0 | 5.1.1 |
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| `r-stitch` | 1.6.10 | 1.7.3 |
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## v1.0.0 - Black Labrador [2024-12-09]
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Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co.re/) template.

‎conf/steps/panel_prep.config

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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:SHAPEIT5_PHASECOMMON' {
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ext.suffix = "vcf.gz"
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ext.prefix = { "${meta.id}_${meta.chunk.replace(':',"_")}_chunks" }
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}
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‎modules.json

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"nf-core": {
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"bcftools/annotate": {
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"branch": "master",
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"git_sha": "cb08035150685b11d890d90c9534d4f16869eaec",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
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},
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"bcftools/concat": {
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"branch": "master",
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"git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/bcftools/concat/bcftools-concat.diff"
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},
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"bcftools/convert": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"bcftools/index": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["bam_impute_glimpse", "vcf_phase_shapeit5"]
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},
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"bcftools/merge": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/bcftools/merge/bcftools-merge.diff"
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},
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"bcftools/mpileup": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "ede1e20af42e2f736638efae1b79762293a6a98a",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/bcftools/mpileup/bcftools-mpileup.diff"
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},
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"bcftools/norm": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"bcftools/pluginsplit": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff"
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},
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"bcftools/query": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"bcftools/stats": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"bcftools/view": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "ede1e20af42e2f736638efae1b79762293a6a98a",
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"installed_by": ["modules"]
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},
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"bedtools/makewindows": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["vcf_phase_shapeit5"]
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},
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"gawk": {
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"branch": "master",
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"git_sha": "caab1314ca62679b629da4c79afa9a4cab2bb8ee",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"glimpse/chunk": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["bam_impute_glimpse"]
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},
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"glimpse/ligate": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["bam_impute_glimpse"]
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},
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"glimpse/phase": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["bam_impute_glimpse"]
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},
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"glimpse2/chunk": {
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"branch": "master",
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"git_sha": "cc64e71652f67ce627064af51008fe0a00850987",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/glimpse2/chunk/glimpse2-chunk.diff"
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"glimpse2/concordance": {
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"branch": "master",
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"git_sha": "6aed50284f6b208fd8eff1ec1dae4b25bf03c432",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"glimpse2/ligate": {
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"branch": "master",
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"git_sha": "cc64e71652f67ce627064af51008fe0a00850987",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"glimpse2/phase": {
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"branch": "master",
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"git_sha": "cc64e71652f67ce627064af51008fe0a00850987",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/glimpse2/phase/glimpse2-phase.diff"
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"quilt/quilt": {
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"branch": "master",
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"git_sha": "82dcdacf8aa932e6683e15a8992ed1cd6fcb174f",
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"git_sha": "9530a622dc5f305410fd68ba86c33a411c07969f",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/quilt/quilt/quilt-quilt.diff"
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},
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"samtools/coverage": {
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"branch": "master",
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
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},
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},
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"samtools/reheader": {
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/reheader/samtools-reheader.diff"
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},
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"samtools/view": {
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"branch": "master",
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
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"git_sha": "b21df1b4e806f7bf3aff0eb41d84453a0025b43e",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/view/samtools-view.diff"
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},
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"shapeit5/ligate": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["vcf_phase_shapeit5"]
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},
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"shapeit5/phasecommon": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["vcf_phase_shapeit5"],
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"patch": "modules/nf-core/shapeit5/phasecommon/shapeit5-phasecommon.diff"
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},
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"stitch": {
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"branch": "master",
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"git_sha": "55e411128ca5036def5dae1aa28a09e3776f59ea",
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"git_sha": "fdc0ff33c44221a72e5ac38d0e21493afe493aff",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/stitch/stitch.diff"
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"tabix/bgzip": {
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"tabix/tabix": {
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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"vcflib/vcffixup": {
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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}

‎modules/nf-core/bcftools/annotate/bcftools-annotate.diff

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‎modules/nf-core/bcftools/annotate/environment.yml

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‎modules/nf-core/bcftools/annotate/main.nf

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‎modules/nf-core/bcftools/annotate/meta.yml

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