Commit d770f29d authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Version 2.1.4

parent 9c4cf485
Pipeline #7375 passed with stages
in 6 minutes and 38 seconds
# v2.1.2
# v2.1.4
**UserFacing**
* Check Design File for spaces in name and file contents
* Update design example, README, and astrocyte.yml with current barcode IDs
......
......@@ -48,19 +48,22 @@ To Run:
* 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.
* 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)
* Last character set in Index references the well position of the 96-well plate that the sample barcode kit is sold in.
* last character set in Index references the well position of the 96-well plate that the sample barcode kit is sold in
* [Current sample barcode IDs](https://s3-us-west-2.amazonaws.com/10x.files/supp/cell-exp/chromium-shared-sample-indexes-plate.csv)
* 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'```
* **--mask**
* add a base mask if the sequencing strategy doesn't match the requirements of 10x Genomics
* eg: **--mask '--use-bases-mask=Y\*,I8n\*,n\*,Y\*'**
* **--outDir**
* optional output directory for run
* eg: ```--outDir 'test'```
......@@ -70,8 +73,8 @@ To Run:
```
* Design example:
| Lane | Sample | Index |
|------|-------------|-----------|
| Lane | Sample | Index |
|------|-------------|----------|
| * | test_sample | SI-GA-C9 |
......
......@@ -32,7 +32,7 @@ bclCount = Channel
.count()
// Define regular variables
pipelineVersion = "2.1.3"
pipelineVersion = "2.1.4"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
......
......@@ -47,6 +47,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript = 'main.nf'
version = '2.1.2'
version = '2.1.4'
nextflowVersion = '>=0.31.0'
}
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