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Change missed single_sample and multi_sample output directories (#…
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…512)

* Change missed  output directory to

* Change missed multi_sample output directory to family

* snv to snvs

* docs
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@fellen31
fellen31 authored Nov 22, 2024
1 parent 07df8fe commit 1e5a25b
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Showing 8 changed files with 68 additions and 80 deletions.
2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -97,6 +97,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#506](https://github.com/genomic-medicine-sweden/nallo/pull/506) - Updated documentation
- [#507](https://github.com/genomic-medicine-sweden/nallo/pull/507) - Changed the default value of `ch_hgnc_ids` to allow running without `--filter_variants_hgnc_ids` introduced in [#496](https://github.com/genomic-medicine-sweden/nallo/pull/443)
- [#509](https://github.com/genomic-medicine-sweden/nallo/pull/509) - Updated documentation to fix mistakes
- [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed one `single_sample` to `sample` and one `multi_sample` to `family` output directories missed in [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502)
- [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed all `*_snv_*` to `*_snvs_*` for published output files to match `snvs`, `cnvs`, `svs` and `repeats`.
- [#513](https://github.com/genomic-medicine-sweden/nallo/pull/513) - Updated CITATIONS.md link in README

### `Removed`
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2 changes: 1 addition & 1 deletion conf/modules/call_cnvs.config
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Expand Up @@ -42,7 +42,7 @@ process {
'--no-version'
].join(' ')
publishDir = [
path: { "${params.outdir}/svs/single_sample/${meta.id}" },
path: { "${params.outdir}/svs/sample/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
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2 changes: 1 addition & 1 deletion conf/modules/filter_variants.config
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Expand Up @@ -46,7 +46,7 @@ process {
"${params.filter_snvs_expression}"
].join(" ") }
publishDir = [
path: { "${params.outdir}/snvs/multi_sample/${meta.id}" },
path: { "${params.outdir}/snvs/family/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
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2 changes: 1 addition & 1 deletion conf/modules/general.config
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Expand Up @@ -75,7 +75,7 @@ process {
def sample = matcher[0][1]
def extension = matcher[0][2]
def annotated = params.skip_snv_annotation ? "" : (params.skip_rank_variants ? "_annotated" : "_annotated_ranked" )
"${sample}/${sample}_snv${annotated}${extension}"
"${sample}/${sample}_snvs${annotated}${extension}"
}
}
]
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24 changes: 12 additions & 12 deletions docs/output.md
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Expand Up @@ -187,23 +187,23 @@ In general, annotated variant calls are output per family while unannotated call

[Echtvar](https://github.com/brentp/echtvar) and [VEP](https://www.ensembl.org/vep) are used for annotating SNVs, while [CADD](https://cadd.gs.washington.edu/) is used to annotate INDELs with CADD scores.

| Path | Description | Call SNVs | Call & annotate SNVs | Call, annotate and rank SNVs |
| -------------------------------------------------------- | ------------------------------------------------------------------------------ | --------- | -------------------- | ---------------------------- |
| `snvs/sample/{sample}/{sample}_snv_annotated.vcf.gz` | VCF file containing annotated variants with alternative genotypes for a sample | | :white_check_mark: | |
| `snvs/sample/{sample}/{sample}_snv_annotated.vcf.gz.tbi` | Index of the annotated VCF file | | :white_check_mark: | |
| `snvs/family/{family}/{family}_snv_annotated.vcf.gz` | VCF file containing annotated variants per family | | :white_check_mark: | |
| `snvs/family/{family}/{family}_snv_annotated.vcf.gz.tbi` | Index of the annotated VCF file | | :white_check_mark: | |
| Path | Description | Call SNVs | Call & annotate SNVs | Call, annotate and rank SNVs |
| --------------------------------------------------------- | ------------------------------------------------------------------------------ | --------- | -------------------- | ---------------------------- |
| `snvs/sample/{sample}/{sample}_snvs_annotated.vcf.gz` | VCF file containing annotated variants with alternative genotypes for a sample | | :white_check_mark: | |
| `snvs/sample/{sample}/{sample}_snvs_annotated.vcf.gz.tbi` | Index of the annotated VCF file | | :white_check_mark: | |
| `snvs/family/{family}/{family}_snvs_annotated.vcf.gz` | VCF file containing annotated variants per family | | :white_check_mark: | |
| `snvs/family/{family}/{family}_snvs_annotated.vcf.gz.tbi` | Index of the annotated VCF file | | :white_check_mark: | |

#### Ranking

[GENMOD](https://github.com/Clinical-Genomics/genmod) is used to rank the annotated SNVs and INDELs.

| Path | Description | Call SNVs | Call & annotate SNVs | Call, annotate and rank SNVs |
| --------------------------------------------------------------- | -------------------------------------------------------- | --------- | -------------------- | ---------------------------- |
| `snvs/sample/{sample}/{sample}_snv_annotated_ranked.vcf.gz` | VCF file with annotated and ranked variants for a sample | | :white_check_mark: |
| `snvs/sample/{sample}/{sample}_snv_annotated_ranked.vcf.gz.tbi` | Index of the ranked VCF file | | :white_check_mark: |
| `snvs/family/{family}/{family}_snv_annotated_ranked.vcf.gz` | VCF file with annotated and ranked variants per family | | | :white_check_mark: |
| `snvs/family/{family}/{family}_snv_annotated_ranked.vcf.gz.tbi` | Index of the ranked VCF file | | | :white_check_mark: |
| Path | Description | Call SNVs | Call & annotate SNVs | Call, annotate and rank SNVs |
| ---------------------------------------------------------------- | -------------------------------------------------------- | --------- | -------------------- | ---------------------------- |
| `snvs/sample/{sample}/{sample}_snvs_annotated_ranked.vcf.gz` | VCF file with annotated and ranked variants for a sample | | :white_check_mark: |
| `snvs/sample/{sample}/{sample}_snvs_annotated_ranked.vcf.gz.tbi` | Index of the ranked VCF file | | :white_check_mark: |
| `snvs/family/{family}/{family}_snvs_annotated_ranked.vcf.gz` | VCF file with annotated and ranked variants per family | | | :white_check_mark: |
| `snvs/family/{family}/{family}_snvs_annotated_ranked.vcf.gz.tbi` | Index of the ranked VCF file | | | :white_check_mark: |

#### Filtering

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28 changes: 12 additions & 16 deletions tests/samplesheet.nf.test.snap
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Expand Up @@ -477,14 +477,12 @@
"snvs/family/FAM",
"snvs/family/FAM/FAM_snv_annotated_ranked.vcf.gz",
"snvs/family/FAM/FAM_snv_annotated_ranked.vcf.gz.tbi",
"snvs/multi_sample",
"snvs/multi_sample/FAM",
"snvs/multi_sample/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz",
"snvs/multi_sample/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz.tbi",
"snvs/family/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz",
"snvs/family/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz.tbi",
"snvs/sample",
"snvs/sample/HG002_Revio",
"snvs/sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz",
"snvs/sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz.tbi",
"snvs/sample/HG002_Revio/HG002_Revio_snvs_annotated_ranked.vcf.gz",
"snvs/sample/HG002_Revio/HG002_Revio_snvs_annotated_ranked.vcf.gz.tbi",
"snvs/stats",
"snvs/stats/sample",
"snvs/stats/sample/HG002_Revio.vcf.gz.bcftools_stats.txt",
Expand All @@ -497,12 +495,10 @@
"svs/family/FAM/FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz.tbi",
"svs/sample",
"svs/sample/HG002_Revio",
"svs/sample/HG002_Revio/HG002_Revio_cnvs.vcf.gz",
"svs/sample/HG002_Revio/HG002_Revio_cnvs.vcf.gz.tbi",
"svs/sample/HG002_Revio/HG002_Revio_svs.vcf.gz",
"svs/sample/HG002_Revio/HG002_Revio_svs.vcf.gz.tbi",
"svs/single_sample",
"svs/single_sample/HG002_Revio",
"svs/single_sample/HG002_Revio/HG002_Revio_cnvs.vcf.gz",
"svs/single_sample/HG002_Revio/HG002_Revio_cnvs.vcf.gz.tbi",
"visualization_tracks",
"visualization_tracks/HG002_Revio",
"visualization_tracks/HG002_Revio/HG002_Revio_hificnv.copynum.bedgraph",
Expand Down Expand Up @@ -631,7 +627,7 @@
"VcfFile [chromosomes=[chr16], sampleCount=1, variantCount=54, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_snv_annotated_ranked.vcf.gz",
"HG002_Revio_snvs_annotated_ranked.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
],
[
Expand All @@ -642,13 +638,13 @@
"FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz",
"VcfFile [chromosomes=[chr16], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_svs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_cnvs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_svs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
]
],
[
Expand All @@ -674,6 +670,6 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-18T08:53:15.024737825"
"timestamp": "2024-11-22T11:48:49.364619961"
}
}
43 changes: 19 additions & 24 deletions tests/samplesheet_multisample_bam.nf.test.snap
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Expand Up @@ -555,17 +555,15 @@
"snvs/family/FAM",
"snvs/family/FAM/FAM_snv_annotated_ranked.vcf.gz",
"snvs/family/FAM/FAM_snv_annotated_ranked.vcf.gz.tbi",
"snvs/multi_sample",
"snvs/multi_sample/FAM",
"snvs/multi_sample/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz",
"snvs/multi_sample/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz.tbi",
"snvs/family/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz",
"snvs/family/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz.tbi",
"snvs/sample",
"snvs/sample/HG002_Revio_A",
"snvs/sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz",
"snvs/sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz.tbi",
"snvs/sample/HG002_Revio_A/HG002_Revio_A_snvs_annotated_ranked.vcf.gz",
"snvs/sample/HG002_Revio_A/HG002_Revio_A_snvs_annotated_ranked.vcf.gz.tbi",
"snvs/sample/HG002_Revio_B",
"snvs/sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz",
"snvs/sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz.tbi",
"snvs/sample/HG002_Revio_B/HG002_Revio_B_snvs_annotated_ranked.vcf.gz",
"snvs/sample/HG002_Revio_B/HG002_Revio_B_snvs_annotated_ranked.vcf.gz.tbi",
"snvs/stats",
"snvs/stats/sample",
"snvs/stats/sample/HG002_Revio_A.vcf.gz.bcftools_stats.txt",
Expand All @@ -579,18 +577,15 @@
"svs/family/FAM/FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz.tbi",
"svs/sample",
"svs/sample/HG002_Revio_A",
"svs/sample/HG002_Revio_A/HG002_Revio_A_cnvs.vcf.gz",
"svs/sample/HG002_Revio_A/HG002_Revio_A_cnvs.vcf.gz.tbi",
"svs/sample/HG002_Revio_A/HG002_Revio_A_svs.vcf.gz",
"svs/sample/HG002_Revio_A/HG002_Revio_A_svs.vcf.gz.tbi",
"svs/sample/HG002_Revio_B",
"svs/sample/HG002_Revio_B/HG002_Revio_B_cnvs.vcf.gz",
"svs/sample/HG002_Revio_B/HG002_Revio_B_cnvs.vcf.gz.tbi",
"svs/sample/HG002_Revio_B/HG002_Revio_B_svs.vcf.gz",
"svs/sample/HG002_Revio_B/HG002_Revio_B_svs.vcf.gz.tbi",
"svs/single_sample",
"svs/single_sample/HG002_Revio_A",
"svs/single_sample/HG002_Revio_A/HG002_Revio_A_cnvs.vcf.gz",
"svs/single_sample/HG002_Revio_A/HG002_Revio_A_cnvs.vcf.gz.tbi",
"svs/single_sample/HG002_Revio_B",
"svs/single_sample/HG002_Revio_B/HG002_Revio_B_cnvs.vcf.gz",
"svs/single_sample/HG002_Revio_B/HG002_Revio_B_cnvs.vcf.gz.tbi",
"visualization_tracks",
"visualization_tracks/HG002_Revio_A",
"visualization_tracks/HG002_Revio_A/HG002_Revio_A_hificnv.copynum.bedgraph",
Expand Down Expand Up @@ -807,11 +802,11 @@
"VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=55, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_A_snv_annotated_ranked.vcf.gz",
"HG002_Revio_A_snvs_annotated_ranked.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_B_snv_annotated_ranked.vcf.gz",
"HG002_Revio_B_snvs_annotated_ranked.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
],
[
Expand All @@ -823,20 +818,20 @@
"VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=5, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_A_svs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
"HG002_Revio_A_cnvs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_B_svs.vcf.gz",
"HG002_Revio_A_svs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_A_cnvs.vcf.gz",
"HG002_Revio_B_cnvs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]"
],
[
"HG002_Revio_B_cnvs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]"
"HG002_Revio_B_svs.vcf.gz",
"VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
]
],
[
Expand Down Expand Up @@ -874,6 +869,6 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-18T08:55:12.484845801"
"timestamp": "2024-11-22T11:48:57.369487572"
}
}
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