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Merge pull request #1472 from maxulysse/string_not_int
fix(vep_cache_version-snpeff_db): both params are string
2 parents 5f7cf6b + 3a36872 commit fa504be

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‎CHANGELOG.md

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
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- [#1422](https://github.com/nf-core/sarek/pull/1422) - Refactoring following `TEMPLATE` sync with `tools` `2.13`
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- [#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
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- [#1439](https://github.com/nf-core/sarek/pull/1439) - Replacing the local module `BUILD_INTERVALS` with the nf-core module `GAWK`
38-
- [#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
38+
- [#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
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- [#1457](https://github.com/nf-core/sarek/pull/1457) - Update all modules
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- [#1466](https://github.com/nf-core/sarek/pull/1466) - Update `VEP`
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@@ -62,6 +62,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
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- [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `snpeff_db` params to `validationSchemaIgnoreParams` to fix issues with Seqera Platform
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- [#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)
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- [#1471](https://github.com/nf-core/sarek/pull/1471) - Update `vep_version` params match the actual tool version
65+
- [#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
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### Removed
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‎conf/igenomes.config

Lines changed: 24 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -36,9 +36,9 @@ params {
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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'
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mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
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ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
39-
snpeff_db = 87
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snpeff_db = '87'
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snpeff_genome = 'GRCh37'
41-
vep_cache_version = 111
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vep_cache_version = '111'
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vep_genome = 'GRCh37'
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vep_species = 'homo_sapiens'
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}
@@ -73,9 +73,9 @@ params {
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pon = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz"
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pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
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sentieon_dnascope_model = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
76-
snpeff_db = 105
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snpeff_db = '105'
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snpeff_genome = 'GRCh38'
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vep_cache_version = 110
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vep_cache_version = '110'
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vep_genome = 'GRCh38'
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vep_species = 'homo_sapiens'
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}
@@ -84,19 +84,19 @@ params {
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fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
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ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
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readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
87-
snpeff_db = 87
87+
snpeff_db = '87'
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snpeff_genome = 'GRCh37'
89-
vep_cache_version = 111
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vep_cache_version = '111'
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vep_genome = 'GRCh37'
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vep_species = 'homo_sapiens'
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}
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'NCBI.GRCh38' {
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bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
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ngscheckmate_bed ="${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed"
97-
snpeff_db = 105
97+
snpeff_db = '105'
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snpeff_genome = 'GRCh38'
99-
vep_cache_version = 111
99+
vep_cache_version = '111'
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vep_genome = 'GRCh38'
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vep_species = 'homo_sapiens'
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}
@@ -118,9 +118,9 @@ params {
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known_indels_tbi = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
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mappability = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
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readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
121-
snpeff_db = 99
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snpeff_db = '99'
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snpeff_genome = 'GRCm38'
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vep_cache_version = 102
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vep_cache_version = '102'
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vep_genome = 'GRCm38'
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vep_species = 'mus_musculus'
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}
@@ -138,28 +138,28 @@ params {
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bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
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readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
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snpeff_db = 75
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snpeff_db = '75'
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snpeff_genome = 'UMD3.1'
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vep_cache_version = 94
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vep_cache_version = '94'
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vep_genome = 'UMD3.1'
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vep_species = 'bos_taurus'
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}
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'WBcel235' {
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bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
150-
snpeff_db = 105
150+
snpeff_db = '105'
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snpeff_genome = 'WBcel235'
152-
vep_cache_version = 111
152+
vep_cache_version = '111'
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vep_genome = 'WBcel235'
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vep_species = 'caenorhabditis_elegans'
155155
}
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'CanFam3.1' {
157157
bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
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readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
160-
snpeff_db = 99
160+
snpeff_db = '99'
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snpeff_genome = 'CanFam3.1'
162-
vep_cache_version = 104
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vep_cache_version = '104'
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vep_genome = 'CanFam3.1'
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vep_species = 'canis_lupus_familiaris'
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}
@@ -215,9 +215,9 @@ params {
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'R64-1-1' {
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bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
218-
snpeff_db = 105
218+
snpeff_db = '105'
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snpeff_genome = 'R64-1-1'
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vep_cache_version = 111
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vep_cache_version = '111'
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vep_genome = 'R64-1-1'
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vep_species = 'saccharomyces_cerevisiae'
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}
@@ -243,29 +243,29 @@ params {
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'hg38' {
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bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
246-
snpeff_db = 105
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snpeff_db = '105'
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snpeff_genome = 'GRCh38'
248-
vep_cache_version = 111
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vep_cache_version = '111'
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vep_genome = 'GRCh38'
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vep_species = 'homo_sapiens'
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}
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'hg19' {
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bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
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readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
256-
snpeff_db = 87
256+
snpeff_db = '87'
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snpeff_genome = 'GRCh37'
258-
vep_cache_version = 111
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vep_cache_version = '111'
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vep_genome = 'GRCh37'
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vep_species = 'homo_sapiens'
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}
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'mm10' {
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bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
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fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
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readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
266-
snpeff_db = 99
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snpeff_db = '99'
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snpeff_genome = 'GRCm38'
268-
vep_cache_version = 102
268+
vep_cache_version = '102'
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vep_genome = 'GRCm38'
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vep_species = 'mus_musculus'
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}

‎conf/test.config

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@@ -36,10 +36,10 @@ params {
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known_indels = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
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ngscheckmate_bed = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
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snpeff_cache = null
39-
snpeff_db = 105
39+
snpeff_db = '105'
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snpeff_genome = 'WBcel235'
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vep_cache = null
42-
vep_cache_version = 110
42+
vep_cache_version = '110'
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vep_genome = 'WBcel235'
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vep_species = 'caenorhabditis_elegans'
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@@ -108,7 +108,7 @@ if (System.getenv('PROFILE')) {
108108
} else if ("$PROFILE" == "docker") {
109109
conda.enabled = false
110110
docker.enabled = true
111-
process.containerOptions = '-u $(id -u):$(id -g)'
111+
docker.runOptions = '-u $(id -u):$(id -g)'
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charliecloud.enabled = false
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podman.enabled = false
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shifter.enabled = false

‎conf/test/cache.config

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@@ -116,7 +116,7 @@ if (System.getenv('PROFILE')) {
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} else if ("$PROFILE" == "docker") {
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conda.enabled = false
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docker.enabled = true
119-
process.containerOptions = '-u $(id -u):$(id -g)'
119+
docker.runOptions = '-u $(id -u):$(id -g)'
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charliecloud.enabled = false
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podman.enabled = false
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shifter.enabled = false

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