Update usage as well in docs

Author: Alexander Peltzer

docs/usage.md

@@ -383,21 +383,25 @@ Turn this on to utilize BWA Mem instead of `bwa aln` for alignment. Can be quite
 
 Users can configure to keep/discard/extract certain groups of reads efficiently in the nf-core/eager pipeline. 
 
-### `--bam_analyse_mapped_only`
+### `--bam_retain_unmapped`
 
-This can be used to only keep mapped reads in the BAM file for downstream analysis. By default turned off, where all reads are kept in the bam file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing.
+Specify this to keep also unmapped reads in the BAM file. This is the default setting, only mapping quality filters are applied to all reads. 
 
-### `--bam_discard_unmapped_entirely`
+### `--bam_separate_unmapped`
 
-This discards all unmapped and extracted reads entirely. By default, this is turned off. 
+Separates the mapped and unmapepd reads, keeps only mapped reads in the BAM file for downstream analysis.
 
-### `--bam_keep_all`
+### `--bam_unmapped_to_fastq`
 
-Turned on by default, keeps all reads that were mapped in the dataset.
+Converted unmapped reads in BAM format to compressed FastQ format. 
 
-### `--bam_retain_all_reads`
+### `--bam_discard_unmapped`
 
-Specify this, if you want to filter reads for downstream analysis. This keeps all mapped and unmapped reads in the output, but allows for quality threshold filtering using `--bam_mapping_quality_threshold`.
+Discards unmapped reads in either FastQ or BAM format, depending on the choice of the `--bam_unmapped_rm_type`. 
+
+### `--bam_unmapped_rm_type`
+
+Defines which unmapped read format to discard, options available are `bam` or `fastq.gz`. By default, `fastq.gz` format will be kept and `bam` will be removed.
 
 ### `--bam_mapping_quality_threshold`