#' Clipping adaptor from single end reads
#' @importFrom glue glue
#' @inheritParams param_general
#' @param adaptor .tar file path
#' @export
glue_se_cutadapt <-
function(
head_label,
adaptor,
in_dir = "./fastq",
out_dir = "./fastq"
){
le <- "\\"
fq_ext <- fq_ext
glue("
cutadapt {le}
-a {adaptor} {le}
-o {out_dir}/{head_label}_cl.{fq_ext}.gz {le}
{in_dir}/{head_label}.{fq_ext}.gz {le}
")
}
#' Clipping adaptor from pair end reads
#' @importFrom glue glue
#' @inheritParams param_general
#' @param f_adaptor .tar file path
#' @param r_adaptor .tar file path
#' @param overlap .tar file path
#' @param minimum_length .tar file path
#' @export
glue_pe_cutadapt <-
function(
head_label,
f_adaptor,
r_adaptor,
overlap = 3,
minimum_length = 20,
in_dir = "./fastq",
out_dir = "./fastq"
){
le <- "\\"
fq_ext <- fq_ext
glue("
cutadapt {le}
--pair-filter=any {le}
-O {overlap} {le}
-m {minimum_length} {le}
-a {f_adaptor} {le}
-A {r_adaptor} {le}
-o {out_dir}/{head_label}_cl_1.{fq_ext}.gz {le}
-p {out_dir}/{head_label}_cl_2.{fq_ext}.gz {le}
{in_dir}/{head_label}_1.{fq_ext}.gz {in_dir}/{head_label}_2.{fq_ext}.gz
")
}
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