As part of the genetic demulitplexing #127, we need to map bulk RNAseq data that we will use to discover SNPs in individual samples.
This PR adds a workflow to perform such mapping from bulk samples to create a BAM file and index it. Because the STAR image doesn't contain samtools, we have to do this in two steps, which is a bit annoying, but isn't terrible.
I am not saving/passing along the full STAR output folder, only the BAM file. The other files are small, so it would not be a burden to do that. I would probably in that case leave original file output name (fixed by STAR), and modify the samtools index script to take the directory and output it. But this seemed more direct, especially for a proof of concept.
As part of the genetic demulitplexing #127, we need to map bulk RNAseq data that we will use to discover SNPs in individual samples.
This PR adds a workflow to perform such mapping from bulk samples to create a BAM file and index it. Because the STAR image doesn't contain samtools, we have to do this in two steps, which is a bit annoying, but isn't terrible.
I am not saving/passing along the full STAR output folder, only the BAM file. The other files are small, so it would not be a burden to do that. I would probably in that case leave original file output name (fixed by STAR), and modify the samtools index script to take the directory and output it. But this seemed more direct, especially for a proof of concept.