Update hmm_flagger_end_to_end_with_mapping.wdl

wdls/workflows/hmm_flagger_end_to_end_with_mapping.wdl

@@ -22,7 +22,7 @@ workflow HMMFlaggerEndToEndWithMapping{
         aligner: "Name of the aligner. It can be either minimap2, winnowmap or veritymap. (Default = winnowmap)"
         presetForMapping: "(Required) Paremeter preset should be selected based on aligner and sequencing platform. Common presets are lr:hqae/map-ont for minimap2, map-pb/map-ont for winnowmap and hifi-haploid/hifi-haploid-complete/hifi-diploid/ont-haploid-complete for veritymap"
         alphaTsv : "(Required) The dependency factors for adjusting emission parameters with previous emission. This parameter is a tsv file with 4 rows and 4 columns with no header line. All numbers should be between 0 and 1. (Default = all alpha factors set to 0)"
-        kmerSize: "The kmer size for using minimap2 or winnowmap. With winnowmap kmer size should be 15 and with minimap2 kmer size should be 15 and 25 for using the presets map-ont and lr:hqae/map-ont respectively."
+        kmerSize: "The kmer size for using minimap2 or winnowmap. With winnowmap kmer size should be 15 and with minimap2 kmer size should be 15 and 25 for using the presets map-ont and lr:hqae respectively."
         alignerOptions: "Aligner options. It can be something like '--eqx --cs -Y -L -y' for minimap2/winnowmap. Note that if assembly is diploid and aligner is either minimap2 or winnowmap '-I8g' is necessary. If the reads contain modification tags and these tags are supposed to be present in the final alignment file, alignerOptions should contain '-y' and the aligner should be either minimap2 or winnowmap. If running secphase is enabled it is recommended to add '-p0.5' to alignerOptions; it will keep more secondary alignments so secphase will have more candidates per read. For veritymap '--careful' can be used but not recommended for whole-genome assembly since it increases the runtime dramatically."
         readExtractionOptions: "The options to be used while converting bam to fastq with samtools fastq. If the reads contain epigentic modification tags it is necessary to use '-TMm,Ml,MM,ML'"
         referenceFastaForReadExtraction: "If reads are in CRAM format then the related reference should be passed to this parameter for read extraction."