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nf-core / exoseq

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Configuration - nest assemblies and references #22

Closed marchoeppner closed 6 years ago

marchoeppner commented 6 years ago

At the moment, the config file does not group genome assemblies with e.g. kit targets/baits. Since these are usually relative to a given coordinate system (assembly), these should be grouped. For example:

params {

   genomes {

'hg19' {
        fasta = "/ifs/data/nfs_share/ikmb_repository/references/gatk/bundle/2.8/hg19/ucsc.hg19.fasta"
        dict = "/ifs/data/nfs_share/ikmb_repository/references/gatk/bundle/2.8/hg19/ucsc.hg19.dict"
        dbsnp = "/ifs/data/nfs_share/ikmb_repository/references/gatk/bundle/2.8/hg19/dbsnp_138.hg19.vcf.gz"
        gold = "/ifs/data/nfs_share/ikmb_repository/references/gatk/bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz"
        g1k = "/ifs/data/nfs_share/ikmb_repository/references/gatk/bundle/2.8/hg19/1000G_phase1.indels.hg19.sites.vcf.gz"
        omni = "/ifs/data/nfs_share/ikmb_repository/references/gatk/bundle/2.8/hg19/1000G_omni2.5.hg19.sites.vcf.gz"
        hapmap = "/ifs/data/nfs_share/ikmb_repository/references/gatk/bundle/2.8/hg19/hapmap_3.3.hg19.sites.vcf.gz"
        kits {
                'Nextera' {
                    targets = "/ifs/data/nfs_share/ikmb_repository/references/exomes/nextera_exome_target_2017/nexterarapidcapture_exome_target_v1.2_hg19.interval_list"
                    baits = "/ifs/data/nfs_share/ikmb_repository/references/exomes/nextera_exome_target_2017/nexterarapidcapture_exome_intervals_v1.2_hg19.interval_list"
                }
                'xGen' {
                    targets = "/ifs/data/nfs_share/ikmb_repository/references/exomes/idt_xgen/v1.0/xgen-exome-research-panel-targets.interval_list"
                    baits = "/ifs/data/nfs_share/ikmb_repository/references/exomes/idt_xgen/v1.0/xgen-exome-research-panel-probes.interval_list"
                }
        }
    }
  }
}
apeltzer commented 6 years ago

We now have an extra configuration file metafiles.config that is imported in various profiles and allows setting a single path to the required -metafiles and -kitfiles and thus accompensates this :-)