ccr.RemoveExtraFiles: Clean intermediate files after pipeline execution.

In francescojm/CRISPRcleanR: Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting

Clean intermediate files after pipeline execution.

Description

This function removes from the output data folder intermediate files created by the analysis pipeline run. This is a utility function that runs automatically as part of the ccr.AnalysisPipeline.

Usage

  ccr.RemoveExtraFiles(
    is_web = FALSE,
    file_counts = NULL,
    files_FASTQ_controls = NULL,
    files_FASTQ_samples = NULL,
    files_BAM_controls = NULL,
    files_BAM_samples = NULL,
    outdir_data = NULL
  )

Arguments

is_web	Boolen flag that indicates if the piepline run was part of a web application backend process.
file_counts	A string specifying the path of a tsv file containing the raw sgRNA counts.
files_FASTQ_controls	List of FASTQ files used to generate the counts for the control samples. Each file name should include the path. The argument must be NULL if counts / BAM files are specified as input.
files_FASTQ_samples	List of FASTQ files used to generate the counts for the samples. Each file name should include the path. The argument must be NULL if counts / BAM files are specified as input.
files_BAM_controls	List of BAM files used to generate the counts for the control samples. Each file name should include the path. The argument must be NULL if counts / FASTQ files are specified as input.
files_BAM_samples	List of BAM files used to generate the counts for the samples. Each file name should include the path. The argument must be NULL if counts / FASTQ files are specified as input.
outdir_data	A string specifying folder where all the results data files are stored.

Author(s)

Paolo Cremaschi ([e-mail])

See Also

ccr.AnalysisPipeline

francescojm/CRISPRcleanR documentation built on April 30, 2023, 5:41 a.m.