linting fixes

Author: jfy133

docs/usage.md

@@ -247,7 +247,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
 
 There are two possible ways of supplying input sequencing data to nf-core/eager. The most efficient but more simplistic is supplying direct paths (with wildcards) to your FASTQ or BAM files, with each file or pair being considered a single library and each one run independently. TSV input requires creation of an extra file by the user and extra metadata, but allows more powerful lane and library merging.
 
-##### Direct Input Method
+#### Direct Input Method
 
 This method is where you specify with `--input`, the path locations of FASTQ (optionally gzipped) or BAM file(s). This option is mutually exclusive to the [TSV input method](#tsv-input-method), which is used for more complex input configurations such as lane and library merging.
 
@@ -269,7 +269,7 @@ If you have multiple files in different directories, you can use additional wild
 
 > :warning: It is not possible to run a mixture of single-end and paired-end files in one run with the paths `--input` method! Please see the [TSV input method](#tsv-input-method) for possibilities.
 
-**Please note** the following requirements:https://nf-co.re/atacseq/docs/usage#introduction
+**Please note** the following requirements:
 
 1. Valid file extensions: `.fastq.gz`, `.fastq`, `.fq.gz`, `.fq`, `.bam`.
 2. The path **must** be enclosed in quotes
@@ -281,7 +281,7 @@ If you have multiple files in different directories, you can use additional wild
 6. Due to limitations of downstream tools (e.g. FastQC), sample IDs may be truncated after the first `.` in the name, Ensure file names are unique prior to this!
 7. For input BAM files you should provide a small decoy reference genome with pre-made indices, e.g. the human mtDNA or phiX genome, for the mandatory parameter `--fasta` in order to avoid long computational time for generating the index files of the reference genome, even if you do not actually need a reference genome for any downstream analyses.
 
-##### TSV Input Method
+#### TSV Input Method
 
 Alternatively to the [direct input method](#direct-input-method), you can supply to `--input` a path to a TSV file that contains paths to FASTQ/BAM files and additional metadata. This allows for more complex procedures such as merging of sequencing data across lanes, sequencing runs, sequencing configuration types, and samples.
 
@@ -313,7 +313,7 @@ Column descriptions are as follows:
 - **Colour Chemistry** A number indicating whether the Illumina sequencer the library was sequenced on was a 2 (e.g. Next/NovaSeq) or 4 (Hi/MiSeq) colour chemistry machine. This informs whether poly-G trimming (if turned on) should be performed.
 - **SeqType:** A text string of either 'PE' or 'SE', specifying paired end (with both an R1 [or forward] and R2 [or reverse]) and single end data (only R1 [forward], or BAM). This will affect lane merging if different per library.
 - **Organism:** A text string of the organism name of the sample or 'NA'. This currently has no functionality and can be set to 'NA', but will affect lane/library merging if different per library
-- **Strandedness:** A text string indicating whether the library type is'single' or 'double'. This will affect lane/library merging if different per library.https://nf-co.re/atacseq/docs/usage#introduction
+- **Strandedness:** A text string indicating whether the library type is'single' or 'double'. This will affect lane/library merging if different per library.
 - **UDG_Treatment:** A text string indicating whether the library was generated with UDG treatment - either 'full', 'half' or 'none'. Will affect lane/library merging if different per library.
 - **R1:** A text string of a file path pointing to a forward or R1 FASTQ file. This can be used with the R2 column. File names **must be unique**, even if they are in different directories.
 - **R2:** A text string of a file path pointing to a reverse or R2 FASTQ file, or 'NA' when single end data. This can be used with the R1 column. File names **must be unique**, even if they are in different directories.
@@ -353,7 +353,7 @@ Note the following important points and limitations for setting up:
   - An error will be thrown if you try to merge both PE and SE and also supply `--skip_merging`.
   - If you truly want to mix SE data and PE data but using mate-pair info for PE mapping, please run FASTQ preprocessing mapping manually and supply BAM files for downstream processing by nf-core/eager
   - If you _regularly_ want to run the situation above, please leave a feature     request on github.
-- DamageProfiler, NuclearContamination, MTtoNucRatio and PreSeq are performed on each unique library separately after deduplication (but prior same-treated library merging). 
+- DamageProfiler, NuclearContamination, MTtoNucRatio and PreSeq are performed on each unique library separately after deduplication (but prior same-treated library merging).
 - nf-core/eager functionality such as `--run_trim_bam` will be applied to only   non-UDG (UDG_Treatment: none) or half-UDG (UDG_Treatment: half) libraries. - Qualimap is run on each sample, after merging of libraries (i.e. your values   will reflect the values of all libraries combined - after being damage trimmed   etc.).
 - Genotyping will be typically performed on each `sample` independently, as normally all libraries will have been merged together. However, if you have a   mixture of single-stranded and double-stranded libraries, you will normally need to genotype separately. In this case you **must** give each the SS and DS   libraries _distinct_ `Sample_IDs`; otherwise you will receive a `file  collision` error in steps such as `sexdeterrmine`, and then you will need to   merge these yourself. We will consider changing this behaviour in the future   if there is enough interest.