diff --git a/README.md b/README.md index 6fd4c5c599bb0b0a116c64883f84bb403725c938..c456f760d15b22c6c579562b41e5c68c7f525418 100755 --- a/README.md +++ b/README.md @@ -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'**