[automated] Fix code linting

README.md

@@ -54,7 +54,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
   - `freebayes`
   - `GATK HaplotypeCaller`
   - `Manta`
-  -  IndexCov
+  - IndexCov
   - `mpileup`
   - `MSIsensor-pro`
   - `Mutect2`
@@ -170,7 +170,7 @@ We thank the following people for their extensive assistance in the development
 - [pallolason](https://github.com/pallolason)
 - [Paul Cantalupo](https://github.com/pcantalupo)
 - [Phil Ewels](https://github.com/ewels)
-- [Pierre Lindenbaum][https://github.com/lindenb=
+- [Pierre Lindenbaum]https://github.com/lindenb=
 - [Sabrina Krakau](https://github.com/skrakau)
 - [Sam Minot](https://github.com/sminot)
 - [Sebastian-D](https://github.com/Sebastian-D)

docs/output.md

@@ -581,23 +581,21 @@ The output is scaled to around 1. So a long stretch with values of 1.5 would be
 
 **Output directory: `{outdir}/variantcalling/indexcov/`**
 
-In addition to the  interactive HTML files, `indexcov` outputs a number of text files:
-
-+ `$prefix-indexcov.ped`: a .ped/.fam file with the inferred sex in the appropriate column if the sex chromosomes were found.
-                          the CNX and CNY columns indicating the floating-point estimate of copy-number for those chromosomes.
-                          `bins.out`: how many bins had a coverage value outside of (0.85, 1.15). high values can indicate high-bias samples.
-                          `bins.lo`: number of bins with value < 0.15. high values indicate missing data.
-                          `bins.hi`: number of bins with value > 1.15. 
-                          `bins.in`: number of bins with value inside of (0.85, 1.15)
-                          `p.out`: `bins.out/bins.in`
-                          `PC1...PC5`: PCA projections calculated with depth of autosomes.
-
-+ `$prefix-indexcov.roc`: tab-delimited columns of chrom, scaled coverage cutoff, and $n_samples columns where each indicates the
-                          proportion of 16KB blocks at or above that scaled coverage value.
-+ `$prefix-indexcov.bed.gz`: a bed file with columns of chrom, start, end, and a column per sample where the values indicate there
-                             scaled coverage for that sample in that 16KB chunk.
-
-
+In addition to the interactive HTML files, `indexcov` outputs a number of text files:
+
+- `$prefix-indexcov.ped`: a .ped/.fam file with the inferred sex in the appropriate column if the sex chromosomes were found.
+  the CNX and CNY columns indicating the floating-point estimate of copy-number for those chromosomes.
+  `bins.out`: how many bins had a coverage value outside of (0.85, 1.15). high values can indicate high-bias samples.
+  `bins.lo`: number of bins with value < 0.15. high values indicate missing data.
+  `bins.hi`: number of bins with value > 1.15.
+  `bins.in`: number of bins with value inside of (0.85, 1.15)
+  `p.out`: `bins.out/bins.in`
+  `PC1...PC5`: PCA projections calculated with depth of autosomes.
+
+- `$prefix-indexcov.roc`: tab-delimited columns of chrom, scaled coverage cutoff, and $n_samples columns where each indicates the
+  proportion of 16KB blocks at or above that scaled coverage value.
+- `$prefix-indexcov.bed.gz`: a bed file with columns of chrom, start, end, and a column per sample where the values indicate there
+  scaled coverage for that sample in that 16KB chunk.
 
 #### Manta