Finished output files, draft is ready for review!

Author: jfy133

docs/output.md

@@ -338,15 +338,13 @@ This section gives a brief summary of where to look for what files for downstrea
 Each module has it's own output directory which sit alongside the `MultiQC/` directory from which you opened the report.
 
   * `reference_genome/` - this directory contains the indexing files  of your input reference genome (i.e. the various `bwa` indices, a `samtools`' `.fai` file, and a picard `.dict`), if you used the `--saveReference` flag.
-  * `FastQC/` - this contains the original per-FASTQ FastQC reports that are summarised with MultiQC. These occur in both `html` (the report) and `.zip` format (raw data). The `after
-  * `read_merging/`
-  * `mapping/`
-  * `samtools/`
-  * `deduplication/`
-  * `preseq/`
-  * `qualimap/`
-  * `damageprofiler/
-  * `pmtools/`
-  * `trimmed_bam/`
-
-TODO
+  * `FastQC/` - this contains the original per-FASTQ FastQC reports that are summarised with MultiQC. These occur in both `html` (the report) and `.zip` format (raw data). The `after_clipping` folder contains the same but for after AdapterRemoval.
+  * `read_merging/` - this contains the log files (ending with `.settings`) with raw trimming (and merging) statistics after AdapterRemoval. In the `output` sub-directory, are the output trimmed (and merged) FASTQ files. These you can use for downstream applications such as taxonomic binning for metagenomic studies.
+  * `mapping/` - this contains a sub-directory corresponding to the mapping tool you used, inside of which will be the initial BAM files containing the reads that mapped to your reference genome with no modification (see below). You will also find a corresponding BAM index file (ending in `.csi` or `.bam`). You can use these for downstream applications e.g. if you wish to use a different de-duplication tool not included in EAGER2 (although please feel free to add a new module request on the Github repository's [issue page](https://github.com/nf-core/eager/issues)!). 
+  * `samtools/` - this contains two sub-directories. `stats/` contain the raw mapping statistics files (ending in `.stats`) from directly after mapping. `filter/` contains BAM files that have had a mapping quality filter applied (set by the `--bam_mapping_quality_threshold` flag) and a corresponding index file. Furthermore, if you selected `--bam_discard_unmapped`, you will find your separate file with only unmapped reads in the format you selected. Note unmapped read BAM files will _not_ have an index file.
+  * `deduplication/` - this contains a sub-directory called `dedup/`, inside here are sample specific directories. Each directory contains a BAM file containing mapped reads but with PCR duplicates removed, a corresponding index file and two stats file. `.hist.` contains raw data for a deduplication histogram used for tools like preseq (see below), and the `.log` contains overall summary dedupliction statistics.
+  * `preseq/` - this contains a `.ccurve` file for every BAM file that had enough deduplication statistics to generate a complexity curve for estimating the amount unique reads that will be yield if the library is re-sequenced. You can use this file for plotting e.g. in `R` to find your sequencing target depth.
+  * `qualimap/` - this contains a sub-directory for every sample, which includes a qualimap report and associated raw statistic files. You can open the `.html` file in your internet browser to see the in-depth report (this will be more detailed than in MultiQC). This includes stuff like percent coverage, depth coverage, GC content and so on of your mapped reads.
+  * `damageprofiler/` - this contains sample specific directories containing raw statistics and damage plots from DamageProfiler. The `.pdf` files can be used to visualise C to T miscoding lesions or read length distributions of your mapped reads. All raw statistics used for the PDF plots are contained in the `.txt` files. 
+  * `pmdtools/` this contains raw output statistics of pmdtools (estimates of frequencies of subsititutions), and BAM files which have been filtered to remove reads that do not have a Post-mortem damage (PMD) score of `--pmdtools_threshold`. The BAM files do not have corresponding index files.
+  * `trimmed_bam/` this contains the BAM files with X number of bases trimmed off as defined with the `--bamutils_clip_left` and `--bamutils_clip_right` flags and corresponding index files. You can use these BAM files for downstream analysis such as re-mapping data with more stringent parameters (if you set trimming to remove the most likely places containing damage in the read).