Linting

docs/output.md

@@ -411,4 +411,4 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
 * `trimmed_bam/` this contains the BAM files with X number of bases trimmed off as defined with the `--bamutils_clip_left` and `--bamutils_clip_right` flags and corresponding index files. You can use these BAM files for downstream analysis such as re-mapping data with more stringent parameters (if you set trimming to remove the most likely places containing damage in the read).
 * `genotyping/` this contains all the (gzipped) VCF files produced by your genotyping module. The file suffix will have the genotyping tool name. You will have VCF files corresponding to your deduplicated BAM files, as well as any turned-on downstream processes that create BAMs (e.g. trimmed bams or pmd tools).
 * `MultiVCFAnalyzer` this contains all output from MultiVCFAnalyzer, including SNP calling statistics, various SNP table(s) and FASTA alignment files.
-* `sex_determination/` this contains the output for the sex determination run. This is a single `.tsv` file that includes a table with the Sample Name, the Nr of Autosomal SNPs, Nr of SNPs on the X/Y chromosome, the Nr of reads mapping to the Autosomes, the Nr of reads mapping to the X/Y chromosome, the relative coverage on the X/Y chromosomes, and the standard error associated with the relative coverages. These measures are provided for each bam file, one row per bam. If the `sexdeterrmine_bedfile` option has not been provided, the error bars cannot be trusted, and runtime will be considerably longer. 
+* `sex_determination/` this contains the output for the sex determination run. This is a single `.tsv` file that includes a table with the Sample Name, the Nr of Autosomal SNPs, Nr of SNPs on the X/Y chromosome, the Nr of reads mapping to the Autosomes, the Nr of reads mapping to the X/Y chromosome, the relative coverage on the X/Y chromosomes, and the standard error associated with the relative coverages. These measures are provided for each bam file, one row per bam. If the `sexdeterrmine_bedfile` option has not been provided, the error bars cannot be trusted, and runtime will be considerably longer.