better utf8 to ascii conversion

viash-hub · Feb 11, 2024 · 51cd979 · 51cd979
1 parent f0bb13c
commit 51cd979
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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 <c5><a0>o<c5><a1>i<c4><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<e2><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
@@ -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)