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Commit c1c8d3a0 authored by Jeremy Mathews's avatar Jeremy Mathews
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fix biohpc.config typos and add gtf location to astrocyte params

parent 437126b7
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......@@ -78,21 +78,21 @@ params {
genomesize = 'hs'
chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCh38/genome.fa'
gta = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
gtf = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
}
'GRCh37' {
bwa = '/project/shared/bicf_workflow_ref/GRCh37'
genomesize = 'hs'
chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCh37/genome.fa'
gta = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
gtf = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
}
'GRCm38' {
bwa = '/project/shared/bicf_workflow_ref/GRCm38'
genomesize = 'mm'
chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCm38/genome.fa'
gta = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
gtf = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
}
}
}
......
......@@ -37,6 +37,7 @@ if (params.astrocyte) {
params.bwaIndex = "$referenceLocation/$params.genome"
params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
params.fasta = "$referenceLocation/$params.genome/genome.fa"
params.gtf = "$referenceLocation/$params.genome/gencode.gtf"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.genomeSize = 'hs'
} else if (params.genome == 'GRCm38') {
......@@ -47,6 +48,7 @@ if (params.astrocyte) {
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
params.gtf = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
}
......
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