Skip to content

Commit

Permalink
Merge branch 'dev' into filter-variants
Browse files Browse the repository at this point in the history
  • Loading branch information
@fellen31
fellen31 authored Nov 18, 2024
2 parents 135edc3 + 4817e1f commit b7e45f2
Show file tree
Hide file tree
Showing 23 changed files with 328 additions and 309 deletions.
21 changes: 20 additions & 1 deletion CHANGELOG.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#411](https://github.com/genomic-medicine-sweden/nallo/pull/411) - Updated longphase module to most recent version. ([#409](https://github.com/genomic-medicine-sweden/nallo/issues/409)).
- [#416](https://github.com/genomic-medicine-sweden/nallo/pull/416) - Updated WhatsHap to 2.3 and added the `--use-supplementary` flag to use supplementary reads for phasing by default. Changed modules to use biocontainers instead of custom containers. ([#296](https://github.com/genomic-medicine-sweden/nallo/issues/296))
- [#417](https://github.com/genomic-medicine-sweden/nallo/pull/417) - Updated SNV annotation tests to use correct configuration, and snapshot the md5sum, and summary of the variants
- [#418](https://github.com/genomic-medicine-sweden/nallo/pull/418) - Changed the default value of `--parallel_alignments` from 1 to 8, meaning the pipeline will perform parallel alignment by default
- [#418](https://github.com/genomic-medicine-sweden/nallo/pull/418) - Changed the default value of `--alignment_processes` from 1 to 8, meaning the pipeline will perform parallel alignment by default
- [#422](https://github.com/genomic-medicine-sweden/nallo/pull/422) - Updated nf-core/tools template to v3.0.1
- [#423](https://github.com/genomic-medicine-sweden/nallo/pull/423) - Updated metro map
- [#428](https://github.com/genomic-medicine-sweden/nallo/pull/428) - Changed from using bcftools to SVDB for SV merging
Expand Down Expand Up @@ -136,6 +136,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| | `--filter_variants_hgnc_ids` |
| | `--filter_snvs_expression` |
| | `--filter_svs_expression` |
| `--skip_short_variant_calling` | `--skip_snv_calling` |
| `--skip_assembly_wf` | `--skip_genome_assembly` |
| `--skip_mapping_wf` | `--skip_alignment` |
| `--skip_methylation_wf` | `--skip_methylation_pileups` |
| `--skip_phasing_wf` | `--skip_phasing` |
| `--variant_caller` | `--snv_caller` |
| `--parallel_snv` | `--snv_calling_processes` |
| `--cadd_prescored` | `--cadd_prescored_indels` |
| `--snp_db` | `--echtvar_snv_databases` |
| `--variant_catalog` | `--stranger_repeat_catalog` |
| `--bed` | `--target_regions` |
| `--hificnv_xy` | `--hificnv_expected_xy_cn` |
| `--hificnv_xx` | `--hificnv_expected_xx_cn` |
| `--hificnv_exclude` | `--hificnv_excluded_regions` |
| `--reduced_penetrance` | `--genmod_reduced_penetrance` |
| `--score_config_snv` | `--genmod_score_config_snvs` |
| `--score_config_sv` | `--genmod_score_config_svs` |
| `--parallel_alignments` | `--alignment_processes` |
| `--svdb_dbs` | `--svdb_sv_databases` |

> [!NOTE]
> Parameter has been updated if both old and new parameter information is present.
Expand Down
4 changes: 2 additions & 2 deletions assets/schema_snp_db.json
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_snp_db.json",
"title": "genomic-medicine-sweden/nallo pipeline - params.snp_db schema",
"description": "Schema for the file provided with params.snp_db",
"title": "genomic-medicine-sweden/nallo pipeline - params.echtvar_snv_databases schema",
"description": "Schema for the file provided with params.echtvar_snv_databases",
"type": "array",
"items": {
"type": "object",
Expand Down
6 changes: 3 additions & 3 deletions conf/modules/general.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ process {
}

withName: '.*:NALLO:SPLITUBAM' {
ext.args = { "--split ${params.parallel_alignments}" }
ext.args = { "--split ${params.alignment_processes}" }
publishDir = [
enabled: false
]
Expand Down Expand Up @@ -159,7 +159,7 @@ process {
path: { "${params.outdir}/aligned_reads/${meta.id}" },
// only a single BAM file per sample
saveAs: { filename ->
filename.equals('versions.yml') ? null : (meta.n_files == 1 && params.skip_phasing_wf ? filename : null)
filename.equals('versions.yml') ? null : (meta.n_files == 1 && params.skip_phasing ? filename : null)
}
]
}
Expand All @@ -170,7 +170,7 @@ process {
publishDir = [
path: { "${params.outdir}/aligned_reads/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : (params.skip_phasing_wf ? filename : null) }
saveAs: { filename -> filename.equals('versions.yml') ? null : (params.skip_phasing ? filename : null) }
]
}

Expand Down
2 changes: 1 addition & 1 deletion conf/modules/methylation.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ process {
'--combine-mods',
'--cpg',
'--combine-strands',
!params.skip_phasing_wf ? '--partition-tag HP' : '',
!params.skip_phasing ? '--partition-tag HP' : '',
].join(' ') }
ext.prefix = { "${meta.id}_modkit_pileup" }
publishDir = [
Expand Down
2 changes: 1 addition & 1 deletion conf/modules/qc_aligned_reads.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ process {
ext.args = { [
'--fast-mode',
'--no-per-base',
params.bed ? '' : '--by 500'
params.target_regions ? '' : '--by 500'
].join(' ') }
publishDir = [
path: { "${params.outdir}/qc/mosdepth/${meta.id}" },
Expand Down
54 changes: 27 additions & 27 deletions conf/test.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,37 +21,37 @@ params {
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/'

// References
fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz'
input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv'
bed = params.pipelines_testdata_base_path + 'reference/test_data.bed'
filter_variants_hgnc_ids = params.pipelines_testdata_base_path + 'testdata/hgnc_ids.tsv'
hificnv_xy = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed'
hificnv_xx = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed'
hificnv_exclude = params.pipelines_testdata_base_path + 'reference/empty.bed'
par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed'
trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed'
variant_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json'
vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz'
vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv'
snp_db = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv'
svdb_dbs = params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv'
reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv'
score_config_snv = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini'
score_config_svs = params.pipelines_testdata_base_path + 'reference/rank_model_svs.ini'
variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
variant_consequences_svs = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz'
fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz'
input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv'
target_regions = params.pipelines_testdata_base_path + 'reference/test_data.bed'
filter_variants_hgnc_ids = params.pipelines_testdata_base_path + 'testdata/hgnc_ids.tsv'
hificnv_expected_xy_cn = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed'
hificnv_expected_xx_cn = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed'
hificnv_excluded_regions = params.pipelines_testdata_base_path + 'reference/empty.bed'
par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed'
trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed'
stranger_repeat_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json'
vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz'
vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv'
echtvar_snv_databases = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv'
svdb_sv_databases = params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv'
genmod_reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv'
genmod_score_config_snvs = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini'
genmod_score_config_svs = params.pipelines_testdata_base_path + 'reference/rank_model_svs.ini'
variant_consequences_snvs = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
variant_consequences_svs = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz'

// Pipeline options
parallel_alignments = 2
parallel_snv = 2
preset = "revio"
alignment_processes = 2
snv_calling_processes = 2
preset = "revio"

// Test config options
extra_modkit_options = '--seed 1 --sampling-frac 0.1'
extra_vep_options = '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz'
extra_paraphase_options = '--gene hba'
extra_hifiasm_options = '-f0 -k30 -w30 -D10 -r1 -N1'
extra_modkit_options = '--seed 1 --sampling-frac 0.1'
extra_vep_options = '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz'
extra_paraphase_options = '--gene hba'
extra_hifiasm_options = '-f0 -k30 -w30 -D10 -r1 -N1'
}

// Impose same minimum Nextflow version as in nextflow.config
Expand Down
Loading

0 comments on commit b7e45f2

Please sign in to comment.