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Remove --extra_gvcfs #238

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Jul 1, 2024
Merged

Remove --extra_gvcfs #238

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4d0161f
Remove --extra_gvcfs
fellen31 Jun 28, 2024
da60a60
update snap
fellen31 Jun 28, 2024
30abbc9
Update CHANGELOG.md
fellen31 Jun 28, 2024
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9 changes: 6 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -18,13 +18,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Removed`

- [#238](https://github.com/genomic-medicine-sweden/nallo/pull/238) - Removed the `--extra_gvcfs` parameter

### `Fixed`

### Parameters

| Old parameter | New parameter |
| ------------- | -------------------------- |
| | `--deepvariant_model_type` |
| Old parameter | New parameter |
| --------------- | -------------------------- |
| | `--deepvariant_model_type` |
| `--extra_gvcfs` | |

## v0.2.0 - [2024-06-26]

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15 changes: 0 additions & 15 deletions docs/usage.md
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Expand Up @@ -133,20 +133,6 @@ HG01123,/path/to/HG01123_sniffles.snf
HG01124,/path/to/HG01124_sniffles.snf
```

- For SNVs - prepare a samplesheet with gVCF files from DeepVariant to supply with `--extra_gvcfs`:

> [!NOTE]
> These has to have been generated with the same version of reference genome.

`extra_gvcfs.csv`

```
sample,file
HG01123,/path/to/HG01123.g.vcf.gz
HG01124,/path/to/HG01124.g.vcf.gz
HG01125,/path/to/HG01125.g.vcf.gz
```

- If running without `--skip_call_paralogs`, the reference genome needs to be hg38

- If running without `--skip_mapping_wf`, a VCF of known polymorphic sites (e.g. [sites.hg38.vcg.gz](https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz)) needs to be supplied with `--somalier_sites`, from which sex will be inferred if possible.
Expand Down Expand Up @@ -263,7 +249,6 @@ Different processes may need extra input files
| Parameter | Description | Type | Default | Required | Hidden |
| ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ |
| `dipcall_par` | Provide a bed file of chrX PAR regions for dipcall | `string` | | | |
| `extra_gvcfs` | Extra input files for GLNexus | `string` | | | |
| `extra_snfs` | Extra input files for Sniffles | `string` | | | |
| `tandem_repeats` | Tandem repeat BED-file for sniffles | `string` | | | |
| `trgt_repeats` | BED-file for repeats to be genotyped | `string` | | | |
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1 change: 0 additions & 1 deletion nextflow.config
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Expand Up @@ -14,7 +14,6 @@ params {
bed = null
dipcall_par = null
extra_snfs = null
extra_gvcfs = null
tandem_repeats = null
trgt_repeats = null
snp_db = null
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8 changes: 0 additions & 8 deletions nextflow_schema.json
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Expand Up @@ -392,14 +392,6 @@
"format": "file-path",
"exists": true
},
"extra_gvcfs": {
"type": "string",
"description": "Extra input files for GLNexus",
"pattern": "^\\S+\\.csv$",
"format": "file-path",
"schema": "assets/schema_gvcfs.json",
"exists": true
},
"extra_snfs": {
"type": "string",
"description": "Extra input files for Sniffles",
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18 changes: 0 additions & 18 deletions subworkflows/local/short_variant_calling/main.nf
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@@ -1,7 +1,5 @@
include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant'
include { GLNEXUS } from '../../../modules/nf-core/glnexus'
include { BCFTOOLS_VIEW_REGIONS } from '../../../modules/local/bcftools/view_regions'
include { TABIX_TABIX as TABIX_EXTRA_GVCFS } from '../../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_DV } from '../../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_DV_VCF } from '../../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_GLNEXUS } from '../../../modules/nf-core/tabix/tabix/main'
Expand All @@ -14,7 +12,6 @@ workflow SHORT_VARIANT_CALLING {

take:
ch_bam_bai_bed // channel: [ val(meta), path(bam), path(bai), path(call_region_bed) ]
ch_extra_gvcfs // channel: [ val(meta), path(gvcfs) ]
ch_fasta // channel: [ val(meta), path(fasta) ]
ch_fai // channel: [ val(meta), path(fai) ]
ch_bed // channel: [ val(meta), path(input_bed) ]
Expand All @@ -33,17 +30,6 @@ workflow SHORT_VARIANT_CALLING {
// Collect GVCFs
ch_snp_calls_gvcf = ch_snp_calls_gvcf.mix(DEEPVARIANT.out.gvcf)

// Extra gVCFs
TABIX_EXTRA_GVCFS(ch_extra_gvcfs)

ch_extra_gvcfs
.join(TABIX_EXTRA_GVCFS.out.tbi)
.groupTuple()
.set{ ch_bcftools_view_regions_in }

// This cuts all regions in BED file from extra gVCFS, better than nothing
BCFTOOLS_VIEW_REGIONS( ch_bcftools_view_regions_in, ch_bed )

// DV gVCFs
TABIX_DV(ch_snp_calls_gvcf)

Expand All @@ -52,7 +38,6 @@ workflow SHORT_VARIANT_CALLING {
.join(TABIX_DV.out.tbi.groupTuple())
.set{ bcftools_concat_dv_in }


// Concat into one gVCF per sample & sort
BCFTOOLS_CONCAT_DV ( bcftools_concat_dv_in )
ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_DV.out.versions)
Expand All @@ -79,7 +64,6 @@ workflow SHORT_VARIANT_CALLING {

// Put DV and extra gvCFs together -> send to glnexus
BCFTOOLS_SORT_DV.out.vcf
.concat(BCFTOOLS_VIEW_REGIONS.out.vcf)
.map { meta, gvcf -> [ ['id':'multisample'], gvcf ]}
.groupTuple()
.set{ ch_glnexus_in }
Expand All @@ -91,8 +75,6 @@ workflow SHORT_VARIANT_CALLING {
// Get versions
ch_versions = ch_versions.mix(DEEPVARIANT.out.versions)
ch_versions = ch_versions.mix(GLNEXUS.out.versions)
ch_versions = ch_versions.mix(BCFTOOLS_VIEW_REGIONS.out.versions)
ch_versions = ch_versions.mix(TABIX_EXTRA_GVCFS.out.versions)
ch_versions = ch_versions.mix(TABIX_DV.out.versions)
ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_DV.out.versions)
ch_versions = ch_versions.mix(BCFTOOLS_SORT_DV.out.versions)
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