collate_external_results: Collect Pandora and Eager results

In sidora-tools/eager2poseidon: Automatically fill in Missing Metadata in a Janno File

Collect Pandora and Eager results

Description

Collect Pandora and Eager results

Usage

collate_external_results(
  sample_ids,
  eager_tsv_fn,
  general_stats_fn,
  credentials,
  keep_only = "none",
  trust_uncalibrated_dates = F,
  snp_cutoff,
  ss_suffix
)

Arguments

sample_ids	character. A vector of the Poseidon_IDs to pull from pandora.
eager_tsv_fn	character. Path to the TSV file used as input for the eager run.
general_stats_fn	character. Path to the MultiQC general stats table. Can be found in multiqc/multiqc_data/multiqc_general_stats.txt within the specified eager output directory (--outdir).
credentials	character. Path to a credentials file containing four lines listing the database host, the port of the database server, user and password, respectively. Passed to get_pandora_connection
keep_only	character. Can be set to "none", "single", or "double". If set to 'single; or 'double', will keep only information for libraries with the specified strandedness. If 'none', all information is retained.
trust_uncalibrated_dates	logical. Should any uncalibrated dates in pandora be trusted? If set to TRUE, then quickcalibrate() is used to calibrate these dates on the fly.
snp_cutoff	integer. The minimum number of SNPs used for nuclear contamination results, for the results to be considered trustworthy. Any values from libraries with fewer than this number of SNPs are ignored.
ss_suffix	character. The suffix added to the Sample_Name of single stranded samples for eager processing, if any.

Value

A tibble with the collected results from Pandora and eager.

sidora-tools/eager2poseidon documentation built on May 12, 2023, 11:58 p.m.