dadaist2-metadata

dadaist2-metadata - create a sample sheet from a list of Paired End FASTQ files, that can be used as a template to add further columns. This is automatically called by dadaist2, but it can be used to generate a valid templeate to be extended with more columns.

Author

Andrea Telatin andrea.telatin@quadram.ac.uk

Synopsis

makeSampleSheet [options] -i INPUT_DIR

Parameters

  • -i, –input-directory DIRECTORY

    Directory containing the paired end files in FASTQ format, gzipped or not.

  • -o, –output-file FILE

    Output file, if not specified will be printed to STDOUT.

  • -1, –for-tag (and -2, –rev-tag) TAG

    Identifier for forward and reverse reads (default: _R1 and _R2)

  • -s, id-separator STRING

    Sample name separator (default: _)

  • -f, –field-separator CHAR

    Separator in the output file table (default: \t)

  • -h, –header-first-col COLNAME

    dadaist2-metadata of the first column header (default: #SampleID)

  • –add-full-path

    Add a colum with the absolute path of the sample Reads

  • –add-mock-column COLNAME

    Add an extra column named COLNAME having as value what is specified by --mock-value

  • —mock-value VALUE

    Default value used to fill an optional column (requires --add-mock-column). Default "sample".

  • –version

    Print version and exit.

Source code and documentation

The program is freely available at https://quadram-institute-bioscience.github.io/dadaist2 released under the MIT licence. The website contains further DOCUMENTATION.