build_default_steps_list: Build default tool configuration

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Build default tool configuration

Description

Build default tool configuration

Usage

build_default_steps_list(
  steps = list(pre_fastqc = list(order = 1, step =
    build_default_step_list()$pre_fastqc, threads =
    build_default_step_threads_list()$pre_fastqc, ram =
    build_default_step_ram_list()$pre_fastqc, batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$pre_fastqc,
    verbose = build_default_step_verbose_list()$pre_fastqc, time =
    build_default_step_time_list()$pre_fastqc, args = list()), trimming = list(order = 2,
    step = build_default_step_list()$trimming, threads =
    build_default_step_threads_list()$trimming, 
     ram =
    build_default_step_ram_list()$trimming, batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$trimming,
    verbose = build_default_step_verbose_list()$trimming, time =
    build_default_step_time_list()$trimming, args = list(mean_quality = 0, min_length =
    18, max_length = "", xadapt = "", yadapt = "")), post_fastqc = list(order = 3, step =
    build_default_step_list()$post_fastqc, threads =
    build_default_step_threads_list()$post_fastqc, ram =
    build_default_step_ram_list()$post_fastqc, 
     batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$post_fastqc,
    verbose = build_default_step_verbose_list()$post_fastqc, time =
    build_default_step_time_list()$post_fastqc, args = list()), alignment = list(order =
    4, step = build_default_step_list()$alignment, threads =
    build_default_step_threads_list()$alignment, ram =
    build_default_step_ram_list()$alignment, batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$alignment, 

        verbose = build_default_step_verbose_list()$alignment, time =
    build_default_step_time_list()$alignment, args = list(clean = TRUE, stats = "all",
    coord_sort = FALSE)), pre_alignqc = list(order = 5, step =
    build_default_step_list()$pre_alignqc, threads =
    build_default_step_threads_list()$pre_alignqc, ram =
    build_default_step_ram_list()$pre_alignqc, batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$pre_alignqc,
    verbose = build_default_step_verbose_list()$pre_alignqc, 
     time =
    build_default_step_time_list()$pre_alignqc, args = list()), merge_bam = list(order =
    6, step = build_default_step_list()$merge_bam, threads =
    build_default_step_threads_list()$merge_bam, ram =
    build_default_step_ram_list()$merge_bam, batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$merge_bam,
    verbose = build_default_step_verbose_list()$merge_bam, time =
    build_default_step_time_list()$merge_bam, args = list()), markdups = list(order = 7,
    step = build_default_step_list()$markdups, 
     threads =
    build_default_step_threads_list()$markdups, ram =
    build_default_step_ram_list()$markdups, batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$markdups,
    verbose = build_default_step_verbose_list()$markdups, time =
    build_default_step_time_list()$markdups, args = list(remove_duplicates = FALSE)),
    recalibrate = list(order = 8, step = build_default_step_list()$recalibrate, threads =
    build_default_step_threads_list()$recalibrate, ram =
    build_default_step_ram_list()$recalibrate, 
     batch_config =
    build_default_preprocess_config(), mode = build_default_step_mode_list()$recalibrate,
    verbose = build_default_step_verbose_list()$recalibrate, time =
    build_default_step_time_list()$recalibrate, args = list(clean = TRUE)), post_alignqc
    = list(order = 9, step = build_default_step_list()$post_alignqc, threads =
    build_default_step_threads_list()$post_alignqc, ram =
    build_default_step_ram_list()$post_alignqc, batch_config =
    build_default_preprocess_config(), mode =
    build_default_step_mode_list()$post_alignqc, 
     verbose =
    build_default_step_verbose_list()$post_alignqc, time =
    build_default_step_time_list()$post_alignqc, args = list()))
)

Arguments

steps

List with pipeline step information

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.