Updated docs and changelog

Author: jfy133

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Merged in [nf-core/tools](https://github.com/nf-core/tools) release V1.6 template changes  
 * A lot more automated tests using Travis CI
 * Don't ignore DamageProfiler errors anymore 
+* Added post-mapping filtering statistics module and corresponding MultiQC statistics [#217](https://github.com/nf-core/eager/issues/217)
 
 ### `Fixed`
 * [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)

docs/output.md

@@ -72,6 +72,7 @@ The default columns are as follows:
   * **Seqs** This is from Post-AdapterRemoval FastQC. Represents the number of preprocessed reads in your adapter trimmed (paired end) merged FASTQ file. The loss between this number and the Pre-AdapterRemoval FastQC can give you an idea of the quality of trimming and merging.
   * **%GC** This is from Post-AdapterRemoval FastQC. Represents the average GC of all preprocessed reads in your adapter trimmed (paired end) merged FASTQ file.
   * **Reads Mapped** This is from Samtools. This is the raw number of preprocessed reads mapped to your reference genome _prior_ map quality filtering and deduplication.
+  * **Reads Mapped** This is from Samtools. This is the raw number of preprocessed reads mapped to your reference genome _after_ map quality filtering and deduplication (note the column name does not distinguish itself from prior-map quality filtering, but the post-filter column is always second)
   * **Duplication Rate** This is from DeDup. This is the percentage of overall number of mapped reads that were an exact duplicate of another read. The number of reads removed by DeDup can be calculating this number by mapped reads (if no map quality filtering was applied!)
   * **Coverage** This is from Qualimap. This is the median number of times a base on your reference genome was covered by a read (i.e. depth coverage).. This average includes bases with 0 reads covering that position.
   * **>= 1X** to **>= 5X** These are from Qualimap. This is the percentage of the genome covered at that particular depth coverage.
@@ -233,6 +234,9 @@ The third row 'Mapped' represents the number of reads that found a place that co
 
 The remaining rows will be 0 when running `bwa aln` as these characteristucs of the data are not considered by the algorithm by default.
 
+> **NB:** The Samtools (pre-samtools filter) plots displayed in the MultiQC report shows mapped reads without mapping quality filtering. This will contain reads that can map to multiple places on your reference genome with equal or slightly less mapping quality score. To see how your reads look after mapping quality, look at the FastQC reports in the Samtools (pre-samtools filter). You should expect after mapping quality filtering, that you will have less reads.
+
+
 ### DeDup
 #### Background
 DeDup is a duplicate removal tool which searchs for PCR duplicates and removes them from your BAM file. We remove these duplicates because otherwise you would be artificially increasing your coverage and subsequently confidence in genotyping, by considering these lab artefacts which are not biologically meaningful. DeDup looks for reads with the same start and end coordinates, and whether they have exactly the same sequence. The main difference of DeDup versus e.g. `samtools markduplicates` is that DeDup considers _both_ ends of a read, not just the start position, so it is more precise in removing actual duplicates without penalising often already low aDNA data.