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VDBWRAIR / ngs_mapper

Genome Mapping Pipeline
GNU General Public License v2.0
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Should samplesheet support absolute path to data? #211

Open necrolyte2 opened 8 years ago

necrolyte2 commented 8 years ago

Watching new users use the pipeline and training them made me realize that the samplesheet seems a bit odd in the way it interacts with runsamplesheet.sh.

Right now you provide a path to where you have directories that have read data(fastq and/or sff) runsamplesheet.sh /path/to/data /path/to/samplesheet.tsv

Should we just make runsamplesheet.sh have 1 parameter(samplesheet.tsv) and then move the path into that first column?

necrolyte2 commented 8 years ago

If we do decide to support this, then we would need to have runsamplesheet.sh support both modes. That is, detect if $1 is a samplesheet.tsv path or a directory that contains samples and run accordingly

averagehat commented 8 years ago

Is it possible that the samplesheet and the reads are in different directories?

necrolyte2 commented 8 years ago

Yes. Currently the runsamplesheet.sh supports relative and absolute path for $1