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fix(vep_cache_version-snpeff_db): both params are string #1472

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merged 2 commits into from
Apr 19, 2024
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fix(vep_cache_version-snpeff_db): both params are string #1472

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5703d0e
fix(vep_cache_version-snpeff_db): both params are string
maxulysse Apr 19, 2024
3a36872
feat(CHANGELOG): update CHANGELOG
maxulysse Apr 19, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
- [#1422](https://github.com/nf-core/sarek/pull/1422) - Refactoring following `TEMPLATE` sync with `tools` `2.13`
- [#1431](https://github.com/nf-core/sarek/pull/1431) - Using docker.containerOptions instead of docker.runOptions. Clearing containerOptions for SPARK modules for any kind of supported container engine
- [#1439](https://github.com/nf-core/sarek/pull/1439) - Replacing the local module `BUILD_INTERVALS` with the nf-core module `GAWK`
- [#1456](https://github.com/nf-core/sarek/pull/1456) - Revert usage of docker.runOptions. Add an empty docker.runOptions when using the new `spark` profile
- [#1456](https://github.com/nf-core/sarek/pull/1456), [#1472](https://github.com/nf-core/sarek/pull/1472) - Revert usage of docker.runOptions. Add an empty docker.runOptions when using the new `spark` profile
- [#1457](https://github.com/nf-core/sarek/pull/1457) - Update all modules
- [#1466](https://github.com/nf-core/sarek/pull/1466) - Update `VEP`

Expand All @@ -62,6 +62,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
- [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `snpeff_db` params to `validationSchemaIgnoreParams` to fix issues with Seqera Platform
- [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `vep_cache_version` params to `validationSchemaIgnoreParams` to fix [#1454](https://github.com/nf-core/sarek/issues/1454)
- [#1471](https://github.com/nf-core/sarek/pull/1471) - Update `vep_version` params match the actual tool version
- [#1472](https://github.com/nf-core/sarek/pull/1472) - Cast `snpeff_db` params as a string to fix issues with Seqera Platform, as [#1471](https://github.com/nf-core/sarek/pull/1471) was not working as expected

### Removed

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48 changes: 24 additions & 24 deletions conf/igenomes.config
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,9 @@ params {
known_indels_vqsr = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.indels.b37.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.b37.vcf.gz'
mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
snpeff_db = 87
snpeff_db = '87'
snpeff_genome = 'GRCh37'
vep_cache_version = 111
vep_cache_version = '111'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
}
Expand Down Expand Up @@ -73,9 +73,9 @@ params {
pon = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz"
pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
sentieon_dnascope_model = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
snpeff_db = 105
snpeff_db = '105'
snpeff_genome = 'GRCh38'
vep_cache_version = 110
vep_cache_version = '110'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
Expand All @@ -84,19 +84,19 @@ params {
fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
snpeff_db = 87
snpeff_db = '87'
snpeff_genome = 'GRCh37'
vep_cache_version = 111
vep_cache_version = '111'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
}
'NCBI.GRCh38' {
bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
ngscheckmate_bed ="${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed"
snpeff_db = 105
snpeff_db = '105'
snpeff_genome = 'GRCh38'
vep_cache_version = 111
vep_cache_version = '111'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
Expand All @@ -118,9 +118,9 @@ params {
known_indels_tbi = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
mappability = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
snpeff_db = 99
snpeff_db = '99'
snpeff_genome = 'GRCm38'
vep_cache_version = 102
vep_cache_version = '102'
vep_genome = 'GRCm38'
vep_species = 'mus_musculus'
}
Expand All @@ -138,28 +138,28 @@ params {
bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
snpeff_db = 75
snpeff_db = '75'
snpeff_genome = 'UMD3.1'
vep_cache_version = 94
vep_cache_version = '94'
vep_genome = 'UMD3.1'
vep_species = 'bos_taurus'
}
'WBcel235' {
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 105
snpeff_db = '105'
snpeff_genome = 'WBcel235'
vep_cache_version = 111
vep_cache_version = '111'
vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
}
'CanFam3.1' {
bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
snpeff_db = 99
snpeff_db = '99'
snpeff_genome = 'CanFam3.1'
vep_cache_version = 104
vep_cache_version = '104'
vep_genome = 'CanFam3.1'
vep_species = 'canis_lupus_familiaris'
}
Expand Down Expand Up @@ -215,9 +215,9 @@ params {
'R64-1-1' {
bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 105
snpeff_db = '105'
snpeff_genome = 'R64-1-1'
vep_cache_version = 111
vep_cache_version = '111'
vep_genome = 'R64-1-1'
vep_species = 'saccharomyces_cerevisiae'
}
Expand All @@ -243,29 +243,29 @@ params {
'hg38' {
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 105
snpeff_db = '105'
snpeff_genome = 'GRCh38'
vep_cache_version = 111
vep_cache_version = '111'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
'hg19' {
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
snpeff_db = 87
snpeff_db = '87'
snpeff_genome = 'GRCh37'
vep_cache_version = 111
vep_cache_version = '111'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
}
'mm10' {
bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
snpeff_db = 99
snpeff_db = '99'
snpeff_genome = 'GRCm38'
vep_cache_version = 102
vep_cache_version = '102'
vep_genome = 'GRCm38'
vep_species = 'mus_musculus'
}
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6 changes: 3 additions & 3 deletions conf/test.config
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Expand Up @@ -36,10 +36,10 @@ params {
known_indels = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
ngscheckmate_bed = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
snpeff_cache = null
snpeff_db = 105
snpeff_db = '105'
snpeff_genome = 'WBcel235'
vep_cache = null
vep_cache_version = 110
vep_cache_version = '110'
vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'

Expand Down Expand Up @@ -108,7 +108,7 @@ if (System.getenv('PROFILE')) {
} else if ("$PROFILE" == "docker") {
conda.enabled = false
docker.enabled = true
process.containerOptions = '-u $(id -u):$(id -g)'
docker.runOptions = '-u $(id -u):$(id -g)'
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charliecloud.enabled = false
podman.enabled = false
shifter.enabled = false
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2 changes: 1 addition & 1 deletion conf/test/cache.config
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Expand Up @@ -116,7 +116,7 @@ if (System.getenv('PROFILE')) {
} else if ("$PROFILE" == "docker") {
conda.enabled = false
docker.enabled = true
process.containerOptions = '-u $(id -u):$(id -g)'
docker.runOptions = '-u $(id -u):$(id -g)'
charliecloud.enabled = false
podman.enabled = false
shifter.enabled = false
Expand Down
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