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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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Remove hardcoding in collate_csr_results #139

Closed rdmorin closed 8 months ago

rdmorin commented 1 year ago

The path to the file loaded by collate_csr_results is hard-coded. This should be changed to use the config and the path where this file lives should also be somewhere central. We can discuss in a GAMBL meeting what location makes the most sense.

collate_csr_results = function(sample_table,seq_type_filter = "genome"){
   if(seq_type_filter=="capture"){
     return(sample_table) #result doesn't exist or make sense for this seq_type
   }
   csr = suppressMessages(read_tsv("/projects/rmorin/projects/gambl-repos/gambl-nthomas/results/icgc_dart/mixcr_current/level_3/mixcr_genome_CSR_results.tsv"))
...
Kdreval commented 8 months ago

I will migrate this issue to the appropriate child repo