Check GAMBLR Config. — check_gamblr

Check that the GAMBLR config you have loaded will work in your setup.

check_gamblr_config(
  compare_timestamps = FALSE,
  ssh_session,
  archive_mode = FALSE,
  force_backup = FALSE
)

Arguments

compare_timestamps: Whether the function will compare timestamps on your local files to the remote copy. Only relevant if you are working remotely.
ssh_session: The ssh_session object see get_ssh_session() for more information. Only relevant if you are working remotely.
archive_mode: This is not currently working but the idea here is to keep a GSC archive of GAMBL in sync with the actively updated outputs
force_backup: Boolean parameter set to FALSE per default.

Details

This function is mostly for remote GAMBLRs to ensure they keep their local mirror of the GAMBL data up-to-date.

Examples

check_gamblr_config()
#> # A tibble: 4 × 2
#>   seq_type projection
#>   <chr>    <chr>     
#> 1 capture  grch37    
#> 2 capture  hg38      
#> 3 genome   grch37    
#> 4 genome   hg38      
#> Warning: argument is not an atomic vector; coercing
#> [1] "Multiple wildcards!"
#> [1] "seq_type"   "projection"
#> [1] "all_the_things/slms_3-1.0_vcf2maf-1.3/{seq_type}--projection/deblacklisted/maf/all_slms-3--{projection}.CDS.maf"
#> [1] "Multiple wildcards!"
#> [1] "seq_type"   "projection"
#> [1] "all_the_things/slms_3-1.0_vcf2maf-1.3/{seq_type}--projection/deblacklisted/augmented_maf/all_slms-3--{projection}.CDS.maf"
#> [1] "Multiple wildcards!"
#> [1] "seq_type"   "projection"
#> [1] "all_the_things/cnv_master-1.0/merges/{seq_type}--{projection}.seg"
#> Warning: argument is not an atomic vector; coercing
#> [1] "all_the_things/svar_master-1.0/merges/gridss_manta.genome--{projection}.bedpe"
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--grch37_clean_blacklist.txt
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--hg38_clean_blacklist.txt
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--grch37_clean_blacklist.txt
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--hg38_clean_blacklist.txt
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_capture_results.tsv
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv.gz
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/DESeq2-0.0_salmon-1.0/mrna/vst-matrix-Hugo_Symbol_tidy.tsv
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/capture--grch37.seg
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/capture--hg38.seg
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/genome--grch37.seg
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/genome--hg38.seg
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe
#> OK
#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/svar_master-1.0/merges/gridss_manta.genome--hg38.bedpe
#> OK
#> [1] "DONE!"