Docs: README and CHANGELOG follow-ups

CHANGELOG.md

@@ -12,9 +12,9 @@ Initial release of nf-core/deepmutscan, created with the [nf-core](https://nf-co
 - Samplesheet input of paired-end FASTQ files per library, annotated with `sample`, `type` (`input`, `output`, `wildtype`) and `replicate`
 - Raw read QC with FastQC and MultiQC
 - Read alignment to a gene-sized reference ORF with BWA-MEM (`--fasta`, `--reading_frame`)
-- Filtering of unmapped, secondary, low mapping-quality (default MAPQ < 30) and indel-containing alignments with samtools; wildtype reads are retained for error correction
+- Filtering of unmapped, secondary, low mapping-quality (MAPQ < 30) and indel-containing alignments with samtools; wildtype reads are retained for error correction
 - Read-pair merging with `vsearch --fastq_mergepairs`, re-alignment, coordinate sorting and indexing
-- Light-weight variant counter built on the `pysam` and `polars` libraries in Python, replacing GATK `AnalyzeSaturationMutagenesis` with a column-compatible output, including a minimum base quality (`--base_qual`, default Q40) and read-edge exclusion window (`--min_flank`, default 2 bp)
+- Light-weight variant counter built on the `pysam` and `polars` libraries in Python, replacing `GATK AnalyzeSaturationMutagenesis` with a column-compatible output, including a minimum base quality (`--base_qual`, default Q40) and read-edge exclusion window (`--min_flank`, default 2 bp)
 - Annotation and filtering of variant counts against the programmed mutagenesis library (`--mutagenesis_type` `nnk`, `nns`, `nnh`, `nnn`, `nnk_nns`, `nnk_nns_nnh` or `custom` with `--custom_codon_library`)
 - Single-nucleotide variant sequencing-error correction (`--error_correction`):
   - `false_doubles` (default): error rates estimated from read-linked false double mutant codons, by maximum likelihood (`--false_doubles_method mle`, default) or empirical Bayes (`eb`), within a configurable codon window (`--false_doubles_codon_window`)
@@ -28,7 +28,7 @@ Initial release of nf-core/deepmutscan, created with the [nf-core](https://nf-co
 - Optional output pseudocount for dropout variants (`--output_pseudocount`, default 1; 0 disables), applied to the default estimator and DiMSum
 - Optional interactive 3D variant effect inspection tool built from a user-supplied wildtype structure (`--pdb`)
 - Self-contained, all-in-one run report (`deepmutscan_report.html`) embedding QC, error-correction, fitness, MultiQC and run statistics
-- `test` profile on a 50,000 read-pair subsample of a GID1A nicking-mutagenesis GluePCA experiment, with nf-test snapshot testing, and `test_full` profile on the complete dataset (ENA PRJEB110196); test data and the PDB structure are hosted on [nf-core/test-datasets](https://github.com/nf-core/test-datasets/tree/deepmutscan/testdata)
+- `test` profile on a 50,000 read-pair subsample of a GID1A nicking-mutagenesis GluePCA experiment, with nf-test snapshot testing, and `test_full` profile on the complete dataset (ENA PRJEB110196); test data and the PDB structure are hosted on [nf-core/test-datasets](https://github.com/nf-core/test-datasets/tree/deepmutscan)
 
 ### `Fixed`
 

README.md

@@ -29,7 +29,7 @@ While DNA synthesis and sequencing technologies have advanced substantially, lon
 ## Major features
 
 - End-to-end processing of DMS libraries from shotgun (randomly fragmented) or amplicon short-read sequencing
-- Light-weight variant counter with base-quality and read-edge filters, producing GATK `AnalyzeSaturationMutagenesis`-compatible count tables
+- Light-weight variant counter with base-quality and read-edge filters, replacing `GATK AnalyzeSaturationMutagenesis`
 - Intrinsic sequencing-error correction of single-nucleotide variant counts from read-linked false double mutants (maximum-likelihood or empirical-Bayes estimators), or from additional wildtype template sequencing
 - Library quality control: mutant count heatmaps, positional coverage and mutation-type biases, sequencing-depth rarefaction
 - Fitness estimation with a built-in log-ratio estimator, plus optional [DiMSum](https://github.com/lehner-lab/DiMSum) and [mutscan](https://github.com/fmicompbio/mutscan)