Interop Object

Parses and tidies Illumina InterOp run-QC summaries. Not a DRAGEN output, so it inherits nemo::Tool rather than DragenTool; housed here since it's typically co-located with BCLConvert outputs.

Super class

nemo::Tool -> Interop

Methods

Public methods

• Interop$new()

• Interop$parse_summary()

• Interop$tidy_summary()

• Interop$parse_indexsummary()

• Interop$tidy_indexsummary()

• Interop$parse_imagingtable()

• Interop$tidy_imagingtable()

Inherited methods

• nemo::Tool$filter_files()
• nemo::Tool$get_globs()
• nemo::Tool$get_metadata()
• nemo::Tool$get_tbls()
• nemo::Tool$list_files()
• nemo::Tool$print()
• nemo::Tool$run()
• nemo::Tool$tidy()
• nemo::Tool$write()

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Method new()

Create a new Interop object.

Usage

Interop$new(path = NULL, files_tbl = NULL)

Arguments

path

(character(1))
Output directory of tool. If files_tbl is supplied, this is ignored.

files_tbl

(tibble(n))
Tibble of files from nemo::list_files_dir().

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Method parse_summary()

Parse <run>_summary.csv into a one-row list-column tibble.

Usage

Interop$parse_summary(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_summary()

Tidy <run>_summary.csv.

Usage

Interop$tidy_summary(x)

Arguments

x

(character(1) or tibble())
Path to file or parsed tibble.

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Method parse_indexsummary()

Parse <run>-index_summary.csv into a one-row list-column tibble.

Usage

Interop$parse_indexsummary(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_indexsummary()

Tidy <run>-index_summary.csv.

Usage

Interop$tidy_indexsummary(x)

Arguments

x

(character(1) or tibble())
Path to file or parsed tibble.

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Method parse_imagingtable()

Parse imaging_table.csv[.gz] positionally, skipping its header: grouped columns (e.g. Corrected<A;C;G;T>) have one label for 4 data columns.

Usage

Interop$parse_imagingtable(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_imagingtable()

Tidy imaging_table.csv[.gz].

Usage

Interop$tidy_imagingtable(x)

Arguments

x

(character(1) or tibble())
Path to file or parsed tibble.

Examples

cls <- Interop; tool <- "interop"
# imaging_tables/ holds a .csv and a .csv.gz copy, so its run also
# exercises nemo's `_2` same-table disambiguation.
odir <- tempdir()
obj_sum <- cls$new(system.file("extdata", tool, "summaries", package = "tidydragen"))
obj_sum$run(output_dir = odir, format = "parquet", input_id = "run1")
obj_it <- cls$new(system.file("extdata", tool, "imaging_tables", package = "tidydragen"))
obj_it$run(output_dir = odir, format = "parquet", input_id = "run1")
(lf <- list.files(odir, pattern = "interop_.*parquet", full.names = FALSE))
#> [1] "interop_imagingtable.parquet"           
#> [2] "interop_imagingtable_2.parquet"         
#> [3] "runA_interop_indexsummarydetail.parquet"
#> [4] "runA_interop_indexsummarymain.parquet"  
#> [5] "runA_interop_summarymain.parquet"       
#> [6] "runA_interop_summaryreadlane.parquet"