From 9e65970646daeca4535c293474d07b5b05331b23 Mon Sep 17 00:00:00 2001 From: emmarousseau Date: Thu, 23 May 2024 16:50:43 +0200 Subject: [PATCH] remove utf8 characters in config --- src/umi_tools/umi_tools_dedup/config.vsh.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/umi_tools/umi_tools_dedup/config.vsh.yaml b/src/umi_tools/umi_tools_dedup/config.vsh.yaml index cc5113e8..7c54369a 100644 --- a/src/umi_tools/umi_tools_dedup/config.vsh.yaml +++ b/src/umi_tools/umi_tools_dedup/config.vsh.yaml @@ -115,21 +115,21 @@ argument_groups: description: | Causes two reads that start in the same position on the same strand and having the same UMI to be considered unique if one is spliced - and the other is not. (Uses the ‘N’ cigar operation to test for splicing). + and the other is not. (Uses the 'N' cigar operation to test for splicing). - name: --soft_clip_threshold type: integer description: | Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only a small overhang over the exon junction. By setting this option, you can treat reads with at least this many - bases soft-clipped at the 3’ end as spliced. + bases soft-clipped at the 3' end as spliced. default: 4 - name: --multimapping_detection_method type: string description: | If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting the best read at a given loci. Supported - tags are “NH”, “X0” and “XT”. If not specified, the read with the highest + tags are "NH", "X0" and "XT". If not specified, the read with the highest mapping quality will be selected. - name: --read_length type: boolean_true @@ -161,7 +161,7 @@ argument_groups: description: | Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches this regex. Default ("^[__|Unassigned]") matches - anything which starts with “__” or “Unassigned”. + anything which starts with "__" or "Unassigned". - name: --per_contig type: boolean_true description: |