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solution for gene-level chromosome separated files input #71

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solution for gene-level chromosome separated files input #71

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12a6cbe
Merge pull request #1 from genepi/main
filosi Nov 2, 2022
aa7eb86
Merge branch 'genepi:main' into main
filosi Mar 1, 2023
fc09b44
Merge branch 'genepi:main' into main
filosi Jun 19, 2023
736ddf6
Remove size in creating channel
filosi Jun 19, 2023
bcf3b85
Add list tuple as input for genelevel tests
filosi Jun 19, 2023
e51bab0
Use list indexing for getting basename
filosi Jun 19, 2023
b3f4b2b
Add support for multiple chromosome files for gene level analysis
filosi Jun 19, 2023
22d3217
Add memory increase for gene-test analysis
filosi Jun 19, 2023
48fed75
Merge branch 'genepi:main' into main
filosi Jul 20, 2023
26ed467
Merge branch 'genepi:main' into main
filosi Aug 7, 2023
13a0df4
Merge branch 'genepi:main' into main
filosi Aug 28, 2023
5479838
Merge branch 'main' into feature/gene_level_association
filosi Aug 28, 2023
cc63183
Remove size in creating channel
filosi Jun 19, 2023
246335a
Add list tuple as input for genelevel tests
filosi Jun 19, 2023
1dd64b4
Use list indexing for getting basename
filosi Jun 19, 2023
c387ce2
Add support for multiple chromosome files for gene level analysis
filosi Jun 19, 2023
ed92952
Merge branch 'feature/gene_level_association' of github.com:filosi/nf…
filosi Aug 29, 2023
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1 change: 1 addition & 0 deletions conf/base.config
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Expand Up @@ -5,6 +5,7 @@ process {
memory = { 1.GB * task.attempt }
}


withName: 'VALIDATE_COVARIATES' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
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3 changes: 1 addition & 2 deletions modules/local/regenie_step2_gene_tests.nf
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Expand Up @@ -5,7 +5,7 @@ process REGENIE_STEP2_GENE_TESTS {

input:
path step1_out
tuple val(filename), path(genotyped_plink_file)
tuple val(filename), path(genotyped_plink_file_bed), path(genotyped_plink_file_bim), path(genotyped_plink_file_fam)
val assoc_format
path phenotypes_file
path covariates_file
Expand Down Expand Up @@ -39,7 +39,6 @@ process REGENIE_STEP2_GENE_TESTS {
def writeMasks = params.regenie_write_bed_masks ? "--write-mask" : ''
def joint = params.regenie_gene_joint ? "--joint ${params.regenie_gene_joint}":''
def condition_list = params.regenie_condition_list ? "--condition-list $condition_list_file" : ''

"""
regenie \
--step 2 \
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4 changes: 3 additions & 1 deletion workflows/nf_gwas.nf
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Expand Up @@ -289,7 +289,9 @@ workflow NF_GWAS {

if (genotypes_association_format == 'bed') {

Channel.fromFilePairs(genotypes_association, size: 3).set {step2_gene_tests_ch}
Channel.fromFilePairs(genotypes_association, size:3)
.map { tuple(it[1][0].baseName, it[1][0], it[1][1], it[1][2]) }
.set {step2_gene_tests_ch}

}

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