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Add pangenome test data set keys (#1170)

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* Update seqwish to version 0.7.2

* seqwish can work with a comma-separated list of PAFs

* level with nf-core/modules master branch

* add pangenome test data keys

* the odgi test data lives in its own folder

Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
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Simon Heumos 2022-01-12 19:01:57 +01:00 committed by GitHub
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commit 4cc3921efb
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tests/config/test_data.config
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@ -149,6 +149,19 @@ params {
justhusky_minimal_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" justhusky_minimal_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
} }
'pangenome' {
pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
pangenome_fa_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
pangenome_paf_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
pangenome_seqwish_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
pangenome_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
'odgi' {
pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
}
}
'illumina' { 'illumina' {
test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"