Merge pull request #669 from nf-core/ramPR

Review suggestions on v2.3.0

CHANGELOG.md

@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608)
-- An option to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
+- An option `extract_alignments` to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
 - Fastp and ngsbits output files as input of MultiQC [#647](https://github.com/nf-core/raredisease/pull/647/).
 - Haplocheck output file as input of MultiQC [#662](https://github.com/nf-core/raredisease/pull/662)
 

docs/usage.md

@@ -185,7 +185,7 @@ The mandatory and optional parameters for each category are tabulated below.
 <sup>4</sup>fasta_fai, bwa, bwamem2 and bwameme, if not provided by the user, will be generated by the pipeline when necessary.<br />
 <sup>5</sup>Used only by Sentieon.<br />
 <sup>6</sup>Default value is 40. Used only by fastp.<br />
-<sup>7</sup>Used to limit your analysis to specific contigs. Can be used to remove alignments to unplaced contigs to minimize potential errors. This parameter should be used in conjuction with `extract_alignments` parameter.<br />
+<sup>7</sup>Used to limit your analysis to specific contigs. Can be used to remove alignments to unplaced contigs to minimize potential errors. This parameter should be used in conjunction with the `extract_alignments` parameter.<br />
 
 ##### 2. QC stats from the alignment files