{nemo} is built on top of R’s R6 encapsulated object-oriented programming
implementation, which helps with code organisation. It consists of
several base classes like Config, Tool, and
Workflow which we describe below. Each R6 class can contain
public and private functions and non-functions (fields).
Other R packages like {tidywigits} and {dracarys}
can create their own Tool and Workflow
children classes that inherit (or override) functions from the {nemo}
parent classes. This allows for custom parsers and tidiers for specific
bioinformatic tools and workflows.
Here we use the Tool1 and Workflow1 classes
as examples to illustrate the structure of the package.
Config
A Config object contains functionality for interacting
with YAML configuration files (under inst/config) that
specify the schemas, types, patterns and field descriptions for the
raw input files and tidy output
tbls. See ?Config.
raw
Let’s look at some of the information for the raw Tool1
config, for instance:
tool <- params$tool
workflow <- params$workflow
conf <- Config$new(tool, pkg = "nemo")
conf## #--- Config tool1 ---#
##
## |var |value |
## |:-----|:-----|
## |tool |tool1 |
## |nraw |4 |
## |ntidy |4 |You can access the individual fields in the classic R list-like
manner, using the $ sign.
Patterns are used to fish out the relevant files from a directory listing.
conf$get_raw_patterns() |>
knitr::kable(caption = glue("{tool} raw file patterns."))| name | value |
|---|---|
| table1 | .tool1.table1.tsv$ |
| table2 | .tool1.table2.tsv$ |
| table3 | .tool1.table3.tsv$ |
File descriptions are based on the available open source documentation.
conf$get_raw_descriptions() |>
knitr::kable(caption = glue("{tool} raw file descriptions."))| name | value |
|---|---|
| table1 | Table1 for tool1. |
| table2 | Table2 for tool1. |
| table3 | Table3 for tool1. |
Versions are used to distinguish changes in schema between individual
tool versions. For example, after Tool1 v1.2.3 metrics Y
and Z were added to table1, which is reflected in the
available schemas. For now we are using latest as a default
version based on the most recent schema tests, and any discrepancies we
see are labelled accordingly by the version of the tool that generated a
file with a different schema.
conf$get_raw_versions() |>
knitr::kable(caption = glue("{tool} raw file versions."))| name | value |
|---|---|
| table1 | v1.2.3 |
| table1 | latest |
| table2 | latest |
| table3 | latest |
The raw schemas specify the column name and type (e.g. character
(c), integer (i), float/double
(d)) for each input file:
(s <- conf$get_raw_schemas_all())## # A tibble: 4 × 3
## name version schema
## <chr> <chr> <list>
## 1 table1 v1.2.3 <tibble [5 × 2]>
## 2 table1 latest <tibble [7 × 2]>
## 3 table2 latest <tibble [3 × 2]>
## 4 table3 latest <tibble [2 × 2]>
s |>
dplyr::filter(name == "table1", version == "v1.2.3") |>
dplyr::select("schema") |>
tidyr::unnest("schema")## # A tibble: 5 × 2
## field type
## <chr> <chr>
## 1 SampleID c
## 2 Chromosome c
## 3 Start i
## 4 End i
## 5 metricX dtidy
Now let’s look at some of the information in the tidy
Tool1 config. The difference between raw and tidy configs
is mostly in the column names (they are standardised to lowercase
separated by underscores, i.e. snake_case), and some raw
files get split into multiple tidy tables (e.g. for normalisation
purposes).
Tidy descriptions are the same as the raw descriptions for now.
conf$get_tidy_descriptions() |>
knitr::kable(caption = glue("{tool} tidy file descriptions."))| name | value |
|---|---|
| table1 | Table1 for tool1. |
| table2 | Table2 for tool1. |
| table3 | Table3 for tool1. |
(s <- conf$get_tidy_schemas_all())## # A tibble: 4 × 4
## name version tbl schema
## <chr> <chr> <chr> <list>
## 1 table1 v1.2.3 tbl1 <tibble [5 × 3]>
## 2 table1 latest tbl1 <tibble [7 × 3]>
## 3 table2 latest tbl1 <tibble [3 × 3]>
## 4 table3 latest tbl1 <tibble [5 × 3]>
s |>
dplyr::filter(.data$name == "table1", version == "v1.2.3") |>
dplyr::select("schema") |>
tidyr::unnest("schema")## # A tibble: 5 × 3
## field type description
## <chr> <chr> <chr>
## 1 sample_id c sample ID
## 2 chromosome c chromosome
## 3 start i start position
## 4 end i end position
## 5 metric_x d metric X
Tool
Tool is the main organisation class for all file parsers
and tidiers. It contains functions for parsing and tidying typical
CSV/TSV files (with column names), and TXT files where the column names
are missing. Currently it utilises the very simple
readr::read_delim function from the {readr}
package that reads all the data into memory. See ?Tool.
These simple parsers are used in 80-90% of cases, so in the future we can optimise the parsing if needed with faster packages such as {data.table}, {duckdb-r}/{duckplyr} or {r-polars}.
We can have different Tool children classes that inherit
(or override) functions and fields from the Tool parent
class. For example, we can create a Tool object for
Tool1 as follows:
- Initialise a
Tool1object:
tool1_path <- system.file("extdata/tool1", package = "nemo")
t1 <- nemo::Tool1$new(path = tool1_path)
# each class comes with a print function
t1## #--- Tool tool1 ---#
##
## |var |value |
## |:------|:-------------------------------------------------------------------------|
## |name |tool1 |
## |path |/home/runner/miniconda3/envs/pkgdown_env/lib/R/library/nemo/extdata/tool1 |
## |files |4 |
## |tidied |FALSE |- Its
Configobject is also constructed based on thenamesupplied - this is used internally to find files of interest and infer their schemas:
t1$config## #--- Config tool1 ---#
##
## |var |value |
## |:-----|:-----|
## |tool |tool1 |
## |nraw |4 |
## |ntidy |4 |
t1$config$get_raw_patterns()## # A tibble: 3 × 2
## name value
## <chr> <chr>
## 1 table1 "\\.tool1\\.table1\\.tsv$"
## 2 table2 "\\.tool1\\.table2\\.tsv$"
## 3 table3 "\\.tool1\\.table3\\.tsv$"
t1$config$get_raw_schema("table1", v = "v1.2.3")## # A tibble: 5 × 2
## field type
## <chr> <chr>
## 1 SampleID c
## 2 Chromosome c
## 3 Start i
## 4 End i
## 5 metricX d
# t1$config$get_raw_schema("table1", v = "latest") # default
t1$config$get_tidy_schema("table1", v = "v1.2.3")## # A tibble: 5 × 3
## field type description
## <chr> <chr> <chr>
## 1 sample_id c sample ID
## 2 chromosome c chromosome
## 3 start i start position
## 4 end i end position
## 5 metric_x d metric X
# t1$config$get_tidy_schema("table1", v = "latest") # defaultWe can list files that can be parsed with
list_files():
(lf <- t1$list_files())## # A tibble: 4 × 10
## tool_parser parser bname size lastmodified path pattern prefix schema group
## <glue> <chr> <chr> <fs:> <dttm> <chr> <chr> <glue> <list> <glu>
## 1 tool1_table1 table1 sampleA.tool1.t… 113 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 2 tool1_table1 table1 sampleA.tool1.t… 153 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble> _2
## 3 tool1_table2 table2 sampleA.tool1.t… 70 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 4 tool1_table3 table3 sampleA.tool1.t… 83 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>## tibble [1 × 10] (S3: tbl_df/tbl/data.frame)
## $ tool_parser : 'glue' chr "tool1_table1"
## $ parser : chr "table1"
## $ bname : chr "sampleA.tool1.table1.tsv"
## $ size : 'fs_bytes' num 113
## $ lastmodified: POSIXct[1:1], format: "2025-09-07 13:03:45"
## $ path : chr "/home/runner/miniconda3/envs/pkgdown_env/lib/R/library/nemo/extdata/tool1/v1.2.3/sampleA.tool1.table1.tsv"
## $ pattern : chr "\\.tool1\\.table1\\.tsv$"
## $ prefix : 'glue' chr "sampleA"
## $ schema :List of 1
## ..$ : tibble [7 × 2] (S3: tbl_df/tbl/data.frame)
## .. ..$ field: chr [1:7] "SampleID" "Chromosome" "Start" "End" ...
## .. ..$ type : chr [1:7] "c" "c" "i" "i" ...
## $ group : 'glue' chr ""We can parse and tidy files of interest using the tidy
function. Note that this function is called on the object and not
assigned anywhere:
# this will create a new field tbls containing the tidy data (and optionally
# the 'raw' parsed data)
t1$tidy(tidy = TRUE, keep_raw = TRUE)
t1$tbls## # A tibble: 4 × 11
## tool_parser parser bname size lastmodified path pattern prefix group raw tidy
## <glue> <chr> <chr> <fs:> <dttm> <chr> <chr> <glue> <glu> <list> <list>
## 1 tool1_table1 table1 sample… 113 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble> <tibble>
## 2 tool1_table1 table1 sample… 153 2025-09-07 13:03:45 /hom… "\\.to… sampl… _2 <tibble> <tibble>
## 3 tool1_table2 table2 sample… 70 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble> <tibble>
## 4 tool1_table3 table3 sample… 83 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble> <tibble>
t1$tbls$raw[[1]] |> dplyr::glimpse()## Rows: 3
## Columns: 5
## $ SampleID <chr> "sampleA", "sampleA", "sampleA"
## $ Chromosome <chr> "chr1", "chr2", "chr3"
## $ Start <int> 10, 100, 1000
## $ End <int> 50, 500, 5000
## $ metricX <dbl> 0.1, 0.2, 0.3
# the tidy tibbles are nested to allow for more than one tidy tibble per file
t1$tbls$tidy[[1]][["data"]][[1]] |> dplyr::glimpse()## Rows: 3
## Columns: 5
## $ sample_id <chr> "sampleA", "sampleA", "sampleA"
## $ chromosome <chr> "chr1", "chr2", "chr3"
## $ start <int> 10, 100, 1000
## $ end <int> 50, 500, 5000
## $ metric_x <dbl> 0.1, 0.2, 0.3We can also focus on a subset of files to tidy using the
filter_files() function. The include and
exclude arguments can specify which parsers to include or
exclude in the analysis:
# create new Tool1 object
t2 <- nemo::Tool1$new(path = tool1_path)
t2$files## # A tibble: 4 × 10
## tool_parser parser bname size lastmodified path pattern prefix schema group
## <glue> <chr> <chr> <fs:> <dttm> <chr> <chr> <glue> <list> <glu>
## 1 tool1_table1 table1 sampleA.tool1.t… 113 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 2 tool1_table1 table1 sampleA.tool1.t… 153 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble> _2
## 3 tool1_table2 table2 sampleA.tool1.t… 70 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 4 tool1_table3 table3 sampleA.tool1.t… 83 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
t2$filter_files(include = c("tool1_table2", "tool1_table3"))
t2$files## # A tibble: 2 × 10
## tool_parser parser bname size lastmodified path pattern prefix schema group
## <glue> <chr> <chr> <fs:> <dttm> <chr> <chr> <glue> <list> <glu>
## 1 tool1_table2 table2 sampleA.tool1.t… 70 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 2 tool1_table3 table3 sampleA.tool1.t… 83 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>After tidying the data of interest, we can write the tidy tibbles to
various formats, like Apache Parquet, PostgreSQL, CSV/TSV and R’s RDS.
Below we can see that the id specified is added to the
written files in an additional nemo_id column. This can be
used e.g. to distinguish results from different runs in a data pipeline.
When writing to a database like PostgreSQL, another column
nemo_pfix is used to distinguish results from the same run
from the same tool.
t2$tidy() # first need to tidy
outdir1 <- tempdir()
fmt <- "csv"
t2$write(odir = outdir1, format = fmt, id = "run123")
wfiles <- fs::dir_info(outdir1) |> dplyr::select(1:5)
wfiles |>
dplyr::mutate(bname = basename(.data$path)) |>
dplyr::select("bname", "size", "type")## # A tibble: 18 × 3
## bname size type
## <chr> <fs::bytes> <fct>
## 1 filefff15044b64 4.71K file
## 2 filefff199777b 4.71K file
## 3 filefff1c267643 4.71K file
## 4 filefff212c0b9f 4.71K file
## 5 filefff244c73ec 4.71K file
## 6 filefff2e5423f0 4.71K file
## 7 filefff49e685f7 4.71K file
## 8 filefff608d94c3 4.71K file
## 9 filefff625b69f5 4.71K file
## 10 filefff6766b1f5 4.71K file
## 11 filefff69c53be3 4.71K file
## 12 filefff72df5f5b 4.71K file
## 13 filefff916ac26 4.71K file
## 14 filefff9763ad7 4.71K file
## 15 filefffce755cd 4.71K file
## 16 rmarkdown-strfff35ffc4b1.html 1.12K file
## 17 sampleA_tool1_table2.csv.gz 80 file
## 18 sampleA_tool1_table3.csv.gz 92 file
# readr::read_csv(wfiles$path[1], show_col_types = F) # see bug #137The nemofy function is a convenient wrapper for the
process of filtering, tidying, and writing.
t3 <- nemo::Tool1$new(path = tool1_path)
outdir2 <- file.path(tempdir(), "t3") |> fs::dir_create()
t3$files## # A tibble: 4 × 10
## tool_parser parser bname size lastmodified path pattern prefix schema group
## <glue> <chr> <chr> <fs:> <dttm> <chr> <chr> <glue> <list> <glu>
## 1 tool1_table1 table1 sampleA.tool1.t… 113 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 2 tool1_table1 table1 sampleA.tool1.t… 153 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble> _2
## 3 tool1_table2 table2 sampleA.tool1.t… 70 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 4 tool1_table3 table3 sampleA.tool1.t… 83 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
t3$nemofy(
odir = outdir2,
format = "tsv",
id = "run_t3"
)
wfiles2 <- fs::dir_info(outdir2) |>
dplyr::mutate(bname = basename(.data$path))
wfiles2 |>
dplyr::select("bname", "size", "type")## # A tibble: 4 × 3
## bname size type
## <chr> <fs::bytes> <fct>
## 1 sampleA_2_tool1_table1.tsv.gz 124 file
## 2 sampleA_tool1_table1.tsv.gz 105 file
## 3 sampleA_tool1_table2.tsv.gz 80 file
## 4 sampleA_tool1_table3.tsv.gz 92 file
readr::read_tsv(wfiles2$path[2], show_col_types = F)## # A tibble: 3 × 6
## nemo_id sample_id chromosome start end metric_x
## <chr> <chr> <chr> <dbl> <dbl> <dbl>
## 1 run_t3 sampleA chr1 10 50 0.1
## 2 run_t3 sampleA chr2 100 500 0.2
## 3 run_t3 sampleA chr3 1000 5000 0.3
Workflow
A Workflow consists of a list of one or more
Tools. We can construct a certain Workflow
with different Tools, which would allow parsing and writing
tidy tables from a variety of bioinformatic tools. See
?Workflow.
For example, {nemo} contains a Workflow1 class as a
Workflow child (containing only a single Tool1
for simplicity). Similarly to Tool, a Workflow
object contains functions such as filter_files,
list_files, tidy, write and
nemofy:
w <- system.file("extdata/tool1", package = "nemo") |>
nemo::Workflow1$new()
outdir3 <- file.path(tempdir(), "oa") |> fs::dir_create()
w$list_files()## # A tibble: 4 × 10
## tool_parser parser bname size lastmodified path pattern prefix schema group
## <glue> <chr> <chr> <fs:> <dttm> <chr> <chr> <glue> <list> <glu>
## 1 tool1_table1 table1 sampleA.tool1.t… 113 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 2 tool1_table1 table1 sampleA.tool1.t… 153 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble> _2
## 3 tool1_table2 table2 sampleA.tool1.t… 70 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
## 4 tool1_table3 table3 sampleA.tool1.t… 83 2025-09-07 13:03:45 /hom… "\\.to… sampl… <tibble>
x <- w$nemofy(
odir = outdir3,
format = "tsv",
id = "workflow1_run1"
)
wfiles3 <- fs::dir_info(outdir3) |>
dplyr::select(1:5) |>
dplyr::mutate(bname = basename(.data$path))
wfiles3 |>
dplyr::select("bname", "size", "type")## # A tibble: 4 × 3
## bname size type
## <chr> <fs::bytes> <fct>
## 1 sampleA_2_tool1_table1.tsv.gz 133 file
## 2 sampleA_tool1_table1.tsv.gz 111 file
## 3 sampleA_tool1_table2.tsv.gz 88 file
## 4 sampleA_tool1_table3.tsv.gz 100 file
readr::read_tsv(wfiles3$path[1], show_col_types = F)## # A tibble: 3 × 8
## nemo_id sample_id chromosome start end metric_x metric_y metric_z
## <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 workflow1_run1 sampleA chr1 10 50 0.1 0.4 0.7
## 2 workflow1_run1 sampleA chr2 100 500 0.2 0.5 0.8
## 3 workflow1_run1 sampleA chr3 1000 5000 0.3 0.6 0.9