diff --git a/src/umi_tools/umi_tools_dedup/config.vsh.yaml b/src/umi_tools/umi_tools_dedup/config.vsh.yaml index 5b03a6e5..50a5d624 100644 --- a/src/umi_tools/umi_tools_dedup/config.vsh.yaml +++ b/src/umi_tools/umi_tools_dedup/config.vsh.yaml @@ -58,7 +58,7 @@ argument_groups: in the file names. - name: --extract_umi_method type: string - choices: ["read_id", "tag", "umis"] + choices: [read_id, tag, umis] description: | Specify the method by which the barcodes were encoded in the read. The options are: @@ -75,7 +75,7 @@ argument_groups: type: string description: | The separator used to separate the UMI from the read sequence. - This is only required if the extract_umi_method is set to id_read. ['_'] + This is only required if the extract_umi_method is set to id_read. [_] example: '_' - name: --umi_tag_split type: string @@ -103,7 +103,7 @@ argument_groups: arguments: - name: --method type: string - choices: ["unique", "percentile", "cluster", "adjacency", "directional"] + choices: [unique, percentile, cluster, adjacency, directional] description: | The method to use for grouping reads. The options are: @@ -211,7 +211,7 @@ argument_groups: example: "discard" - name: --chimeric_pairs type: string - choices: ["discard", "use", "output"] + choices: [discard, use, output] description: | How chimeric pairs should be handled. The options are: @@ -221,7 +221,7 @@ argument_groups: example: "use" - name: --unpaired_reads type: string - choices: ["discard", "use", "output"] + choices: [discard, use, output] description: | How unpaired reads should be handled. The options are: