diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml index 24105a88d79683610430ccf86b5b84b3335f226d..4f831151548dd639109b2ec5c168e3d54c862944 100755 --- a/astrocyte_pkg.yml +++ b/astrocyte_pkg.yml @@ -149,7 +149,7 @@ workflow_parameters: choices: - ['3.1.0', '3.1.0'] - ['3.0.2', '3.0.2'] - - ['3.0.1', '3.0.1'] + - ['2.2.0', '2.2.0'] - ['2.1.1', '2.1.1'] required: true description: | diff --git a/docs/index.md b/docs/index.md index 2532ad93b5637d778c0804449c7f3bf1afe1214a..579590bd9837e5e6478c64d5cca4bbb3df00543b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -48,17 +48,16 @@ To Run: * if --expextedCells is used then --forceCells is not necessary * only used if force cells is not entered or set to 0 * **force cells** - * Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells. - * 0-10000 - * if force cells is used then expected cells is not necessary and is ignored + * Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells. + * 0-10000 + * if force cells is used then expected cells is not necessary and is ignored * **chemistry version** * 10x single cell gene expression chemistry version (only used in cellranger version 3.x). * setting to auto will attempt to autodetect from the detected cycle strategy in the fastq's - * chemistry version is only used if cellranger version is > 2.x - * cellranger version 2.1.1 can only read chemistry version less than or equal to two (2) + * cellranger version 2.x cannot read chemistry version 3prime GEX v3 * **cellranger version** * 10x cellranger version. - * cellranger version 2.1.1 can only read chemistry version less than or equal to two (2) + * cellranger version 2.x cannot read chemistry version 3prime GEX v3 * Design example: