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CCBR / Pipeliner

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
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GUI Warning Message: Whole Exome/Genome Pipelines #377

Closed skchronicles closed 5 years ago

skchronicles commented 5 years ago

GUI Warning Message: Whole Exome/Genome Pipelines

mm9 is not supported by the whole genome/exome pipelines. If you look at the mm9.json file, it is actually using mm10 reference files:

{
    "references": {
        "exomeseq": {
            "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
            "PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_dbSNP_allStrains_compSet.vcf.gz",
            "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
            "CHROMS": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chrX","chrY","chrM"],
            "INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
            "KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
            "KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix",

"genomeseq": {
            "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
            "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
            "CHROMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_chromosomes",
            "INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
            "KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
            "KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
            "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix",
            "CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
            "SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",

Solution: Adding a pop-up box to warning users if they select the wrong reference genome.

skchronicles commented 5 years ago

Closed

Pushed changes to activeDev: