Perform Cytoscans/Oncoscans CNV analysis with EaCoN

public 1yr ago Version: v1.2 0 bookmarks

View Workflow

This is the Snakemake workflow for CEL Oncoscan/Cytoscan analysis, powered by EaCoN .

Each tool belong to their respective authors.

See wiki for more information.

For additional informations, see STRonGR

Code Snippets

    script:
        "../scripts/EaCoN_process.R"


"""
This rule performs segmentation
"""

SnakeMake From line 46 of rules/eacon.smk

    script:
        "../scripts/EaCoN_segment.R"


"""
This rule tries to build a copy number model
"""

SnakeMake From line 98 of rules/eacon.smk

    script:
        "../scripts/EaCoN_ascn.R"


"""
This rule covers instability score
"""

SnakeMake From line 141 of rules/eacon.smk

    wrapper:
        "/bio/eacon/instability"


"""
This rule writes a HTML report
"""

SnakeMake From line 174 of rules/eacon.smk

script:
    "../scripts/EaCoN_annotate.R"

SnakeMake From line 232 of rules/eacon.smk

library("EaCoN");
library("devtools");

Sys.setenv(
  PATH = paste(
    Sys.getenv("PATH"),
    snakemake@config[["params"]][["scripts"]],
    sep=":"
  )
);

EaCoN::Annotate.ff(
  RDS.file = snakemake@input[["rds"]],
  author.name = "STRonGR",
  ldb = snakemake@config[["params"]][["ldb"]],
  solo = TRUE
);

R devtools EaCoN From line 3 of scripts/EaCoN_annotate.R

library("EaCoN");

EaCoN::ASCN.ff(
  RDS.file = snakemake@input[["rds"]],
  force = TRUE
);

R EaCoN From line 3 of scripts/EaCoN_ascn.R

library("EaCoN");

if ("ATChannelCel" %in% names(snakemake@input)) {
  EaCoN::OS.Process(
    ATChannelCel = snakemake@input[["ATChannelCel"]],
    GCChannelCel = snakemake@input[["GCChannelCel"]],
    samplename = snakemake@wildcards[["sample"]],
    apt.build = snakemake@config[["params"]][["nar"]],
    force = TRUE
  );
} else {
  EaCoN::CS.Process(
    CEL = snakemake@input[["CEL"]],
    samplename = snakemake@wildcards[["sample"]],
    force = TRUE
  );
}

R EaCoN From line 3 of scripts/EaCoN_process.R

library("EaCoN");

smooth_k <- base::as.numeric(snakemake@config[["params"]][["smooth_k"]]);
if ((is.null(snakemake@config[["params"]][["smooth_k"]])) | (snakemake@config[["params"]][["smooth_k"]] == 'NULL')) {
  smooth_k <- NULL;
}

EaCoN::Segment.ff(
  RDS.file = snakemake@input[["rds"]],
  segmenter = snakemake@config[["params"]][["segmenter"]],
  smooth.k = smooth_k,
  BAF.filter = base::as.numeric(snakemake@config[["params"]][["baf_filter"]]),
  SER.pen = base::as.numeric(snakemake@config[["params"]][["ser_pen"]]),
  nrf = base::as.numeric(snakemake@config[["params"]][["nrf"]]),
  penalty = base::as.numeric(snakemake@config[["params"]][["penalty"]]),
  force = TRUE
);