Handle single primer-trimming #80
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This won't run until single primer handling is included in fgbio (see fulcrumgenomics/fgbio#681). |
…q-varlociraptor into single_primer
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This PR is ready now but we still need to wait for a new release of fgbio before merging. |
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@johanneskoester This PR is finally ready for review as fgbio has been released. |
| @@ -22,6 +22,9 @@ primers: | |||
| # path to fasta files containg primer sequences | |||
| primers_fa1: "path/to/primer-fa1" | |||
| primers_fa2: "path/to/primer-fa2" | |||
| # optional primer file allowing to define primers per sample | |||
| # overwrites primers_fa1 and primers_fa2 | |||
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This needs some explanation on the expected columns of the TSV. Why not just adding a respective column to the units.tsv?
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For a large number of samples there would be a lot redundancy when adding the primer-files to the units.tsv. By using a seperat tsv-file holding the fields panel, fa1, fa2 (optional) primers must only be specified panel-wise.
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Ah, and then in the sample sheet you define the panel? Is this already documented?
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THis should be explained in depth in config/README.md
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Good point. This appeared intuitive to me but it is not.
These are first adjustment of the pipeline when receiving just one primer for trimming.
In this case primers can not be used for region targeting and a separat bed-file is required.
As primers/roi-files often hold coordinates of hg19 a liftover chain url can be defined allowing to perform a liftover for targeted regions.
This will be finalized as soon as fgbio is capable of handling single primers.