diff --git a/src/star/star_align/argument_groups.yaml b/src/star/star_align/argument_groups.yaml index 4ecc001e..b7fcaf98 100644 --- a/src/star/star_align/argument_groups.yaml +++ b/src/star/star_align/argument_groups.yaml @@ -202,7 +202,7 @@ argument_groups: adapter clipping type - Hamming ... adapter clipping based on Hamming distance, with the number of mismatches controlled by --clip5pAdapterMMp - - CellRanger4 ... 5p and 3p adapter clipping similar to CellRanger4. Utilizes Opal package by Martin oi<87>: https://github.com/Martinsos/opal + - CellRanger4 ... 5p and 3p adapter clipping similar to CellRanger4. Utilizes Opal package by Martin Sosic: https://github.com/Martinsos/opal - None ... no adapter clipping, all other clip* parameters are disregarded example: Hamming - name: --clip3pNbases @@ -1083,7 +1083,7 @@ argument_groups: - name: --waspOutputMode type: string description: |- - WASP allele-specific output type. This is re-implementation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061<80><93>1063 (2015), https://www.nature.com/articles/nmeth.3582 . + WASP allele-specific output type. This is re-implementation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061-1063 (2015), https://www.nature.com/articles/nmeth.3582 . - SAMtag ... add WASP tags to the alignments that pass WASP filtering - name: STARsolo (single cell RNA-seq) parameters diff --git a/src/star/star_align/utils/process_params.R b/src/star/star_align/utils/process_params.R index c5e09669..291928ba 100644 --- a/src/star/star_align/utils/process_params.R +++ b/src/star/star_align/utils/process_params.R @@ -9,7 +9,7 @@ yaml_file <- "src/star/star_align/argument_groups.yaml" param_txt <- readr::read_lines(local_file) # replace non-ascii characters with their ascii approximations -param_txt <- iconv(param_txt, "UTF-8", "ASCII", sub = "byte") +param_txt <- iconv(param_txt, "UTF-8", "ASCII//TRANSLIT") dev_begin <- grep("#####UnderDevelopment_begin", param_txt) dev_end <- grep("#####UnderDevelopment_end", param_txt)