Commit 0d93e020 authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Update index.md

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......@@ -15,16 +15,16 @@ To Run:
* Workflow parameters:
* **bcl**
* Base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization).
* There can be multiple basecall files, but they all will be demultiplexed by the same design file.
* REQUIRED
* Base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization).
* There can be multiple basecall files, but they all will be demultiplexed by the same design file.
* REQUIRED
* **design file**
* A design file listing lane, sample, corresponding sample barcode. There can be multiple rows with the same sample name, if there are multiple fastq's for that sample.
* REQUIRED
* column 1 = "Lane" (number of lanes to demultiplex, */** for all lanes)
* column 2 = "Sample" (sample name)
* column 3 = "Index" (10x sample index barcode, eg SI-GA-A1)
* eg: can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
* A design file listing lane, sample, corresponding sample barcode. There can be multiple rows with the same sample name, if there are multiple fastq's for that sample.
* REQUIRED
* column 1 = "Lane" (number of lanes to demultiplex, */** for all lanes)
* column 2 = "Sample" (sample name)
* column 3 = "Index" (10x sample index barcode, eg SI-GA-A1)
* eg: can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
* Design example:
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