Commit b1e7748e authored by Gervaise Henry's avatar Gervaise Henry 🤠

Update README.md

parent bc191ed6
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......@@ -25,27 +25,27 @@ To Run:
* Available parameters:
* **--name**
* run name, puts outputs in a directory with this name
* eg: **--name 'test'**
* run name, puts outputs in a directory with this name
* eg: **--name 'test'**
* **--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.
* eg: **--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'**
* 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.
* eg: **--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'**
* **--designFile**
* path to design file (csv format) location
* 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)
* can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
* can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
* eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'**
* **--outDir**
* optional output directory for run
* eg: **--outDir 'test'**
* FULL EXAMPLE:
**nextflow run workflow/main.nf --name 'test' --bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-simple-1_2_0.csv' --outDir 'test'**
* path to design file (csv format) location
* 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)
* can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
* can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
* eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'**
* **--outDir**
* optional output directory for run
* eg: **--outDir 'test'**
* FULL EXAMPLE:
```
nextflow run workflow/main.nf --name 'test' --bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-simple-1_2_0.csv' --outDir 'test'
```
* Design example:
| Lane | Sample | Index |
......
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