make nf-core/rnaseq manifest from Synapse fileview

gistfile1.txt

library(synapser)
library(dplyr)
synLogin()

##query for files for manifest
query <- "SELECT id, specimenID, readPair FROM syn51907744 where fileFormat = 'fastq'"
key <- "readPair"
value <- "id"

res <- synTableQuery(query, includeRowIdAndRowVersion = F)$asDataFrame() 

res_formatted <- res %>% 
  mutate(id = glue::glue("syn://{id}")) %>% 
  tidyr::spread(key = key, value = value) %>%
  mutate(sample = specimenID,
         fastq_1 = `1`,
         fastq_2 = `2`,
         strandedness = "auto",
         .keep = 'none')

readr::write_csv(res_formatted, "~/downloads/ucf_rnaseq_staging.csv")