Process

Format

cg project_addsample ?options? projectdir samplename rawdata ...

Summary

Add a sample directory to a project directory.

Description

project_addsample is a convenience function to add a sample to a project directory in the proper structure. (You can do the same manually by creating the directories, adding links ot copying raw data files) If the project directoy does not exist yet, it will be created. The command creates a sample directory under projectdir/samples, and adds the given raw data under projectdir/samples/samplename/ori (by default using softlinks).

rawdata can either be given as a single directory (containing the fastq files, Complete Genomics source data, etc. according to the type of experiment) or as one or more files. (see howto_process_project for examples.

Arguments

projectdir: project directory name.
samplename: sample name
rawdata: directory containing source/raw data (for only one sample), or one or more raw data files.

Options

-amplicons ampliconfile: This option turns on amplicon sequencing analysis (see cg process_sample) using the amplicons defained in ampliconfile
-targetfile targetfile: if targetfile is provided, coverage statistics will be calculated for this region
-tranfer soft/rel/hard/copy: determines how raw data files are "transferred" to the sampledir: soft(link absolute path), rel(ative softlink), hard(link) or copy
-force 0/1: Normally an error is given if the target file already exists. use -force 1 to overwrite existing sample data

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