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Commit 603c8398 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Update README.md

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......@@ -24,73 +24,73 @@ To Run:
* Available parameters:
* **--fastq**
* path to the fastq location
* R1 and R2 only necessary but can include I2
* only fastq's in designFile (see below) are used, not present will be ignored
* eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz'**
* path to the fastq location
* R1 and R2 only necessary but can include I2
* only fastq's in designFile (see below) are used, not present will be ignored
* eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz'**
* **--designFile**
* path to design file (csv format) location
* column 1 = "Sample"
* column 2 = "fastq_R1"
* column 3 = "fastq_R2"
* 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_count/blob/master/docs/design.csv)
* eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv'**
* **--genome**
* reference genome
* requires workflow/conf/biohpc.config to work
* name of available 10x Gemomics premade reference genomes:
* *'GRCh38-3.0.0'* = Human GRCh38 release 93
* *'GRCh38-1.2.0'* = Human GRCh38 release 84
* *'hg19-3.0.0'* = Human GRCh37 (hg19) release 87
* *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
* *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 93
* *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 84
* *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
* *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
* *'ercc92-1.2.0'* = ERCC.92 Spike-In
* if --genome is used then --genomeLocationFull is not necessary
* eg: **--genome 'GRCh38-3.0.0'**
* **--genomeLocationFull**
* path to a custom genome
* if --genomeLocationFull is used --genome is not necessary and is ignored
* eg. **--genomeLocationFull '/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0'**
* **--expectCells**
* expected number of cells to be detected
* guides cellranger in it's cutoff for background/low quality cells
* as a guide it doesn't have to be exact
* 0-10000
* if --expextedCells is used then --forceCells is not necessary
* only used if --forceCells is not entered or set to 0
* eg: **--expectCells 10000**
* **--forceCells**
* forces filtering of the top number of cells matching this parameter
* 0-10000
* if --forceCells is used then --expectedCells is not necessary and is ignored
* eg: **--forceCells 10000**
* **--kitVersion**
* the library chemistry version number for the 10x Genomics Gene Expression kit
* setting to auto will attempt to autodetect from the detected sequencing strategy in the fastq's
* version numbers are spelled out
* --kitversion is only used if --version (cellranger version) is > 2
* --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
* options:
* *'auto'*
* *'three'*
* *'two'*
* eg: **--kitVersion 'three'**
* **--version**
* cellranger version
* --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
* options:
* *'3.0.2'*
* *'3.0.1'*
* *'2.1.1'*
* eg: **--version '3.0.2'**'
* **--outDir**
* optional output directory for run
* eg: **--outDir 'test'**
* FULL EXAMPLE:
* path to design file (csv format) location
* column 1 = "Sample"
* column 2 = "fastq_R1"
* column 3 = "fastq_R2"
* 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_count/blob/master/docs/design.csv)
* eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv'**
* **--genome**
* reference genome
* requires workflow/conf/biohpc.config to work
* name of available 10x Gemomics premade reference genomes:
* *'GRCh38-3.0.0'* = Human GRCh38 release 93
* *'GRCh38-1.2.0'* = Human GRCh38 release 84
* *'hg19-3.0.0'* = Human GRCh37 (hg19) release 87
* *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
* *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 93
* *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 84
* *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
* *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
* *'ercc92-1.2.0'* = ERCC.92 Spike-In
* if --genome is used then --genomeLocationFull is not necessary
* eg: **--genome 'GRCh38-3.0.0'**
* **--genomeLocationFull**
* path to a custom genome
* if --genomeLocationFull is used --genome is not necessary and is ignored
* eg. **--genomeLocationFull '/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0'**
* **--expectCells**
* expected number of cells to be detected
* guides cellranger in it's cutoff for background/low quality cells
* as a guide it doesn't have to be exact
* 0-10000
* if --expextedCells is used then --forceCells is not necessary
* only used if --forceCells is not entered or set to 0
* eg: **--expectCells 10000**
* **--forceCells**
* forces filtering of the top number of cells matching this parameter
* 0-10000
* if --forceCells is used then --expectedCells is not necessary and is ignored
* eg: **--forceCells 10000**
* **--kitVersion**
* the library chemistry version number for the 10x Genomics Gene Expression kit
* setting to auto will attempt to autodetect from the detected sequencing strategy in the fastq's
* version numbers are spelled out
* --kitversion is only used if --version (cellranger version) is > 2
* --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
* options:
* *'auto'*
* *'three'*
* *'two'*
* eg: **--kitVersion 'three'**
* **--version**
* cellranger version
* --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
* options:
* *'3.0.2'*
* *'3.0.1'*
* *'2.1.1'*
* eg: **--version '3.0.2'**
* **--outDir**
* optional output directory for run
* eg: **--outDir 'test'**
* FULL EXAMPLE:
**nextflow run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' --outDir 'test'**
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