Add documentation for output docs

docs/output.md

@@ -64,6 +64,8 @@ fastp can automatically detect adapter sequences for Illumina data.
 <summary>Output files</summary>
 
 - `fastp`
+  - `<sample_id>.fastp.fastq.gz`: File with the trimmed unmerged fastq reads.
+  - `<sample_id>.merged.fastq.gz`: File with the reads that were successfully merged.
 
 </details>
 
@@ -95,7 +97,7 @@ Note that the FASTQ files may _not_ always be the 'final' reads that go into tax
 <summary>Output files</summary>
 
 - `porechop`
-  - `<sample_id>.fastq.gz`
+  - `<sample_id>.fastq.gz`: Adapter-trimmed file
 
 </details>
 
@@ -143,8 +145,8 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
 <summary>Output files</summary>
 
 - `filtlong`
-  - `<sample_id>_filtered.fastq.g`
+  - `<sample_id>_filtered.fastq.gz`: Quality or short read data filtered file
-  - `<sample_id>_filtered.log`
+  - `<sample_id>_filtered.log`: log file containing summary statistics
 
 </details>
 
@@ -174,7 +176,7 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
 <summary>Output files</summary>
 
 - `minimap2`
-  - `<sample_id>.bam`
+  - `<sample_id>.bam`: Alignment file in bam format
 
 </details>
 
@@ -184,7 +186,7 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
 <summary>Output files</summary>
 
 - `samtoolsstats`
-  - `<sample_id>.stats`
+  - `<sample_id>.stats`: File containing samtools stats output
 
 </details>
 
@@ -204,7 +206,7 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
 
 </details>
 
-The main taxonomic profiling file from KrakenUniq is the `*.tsv` file. This provides the basic results from Kraken2 but with the corrected abundance information. 
+The main taxonomic profiling file from KrakenUniq is the `*.tsv` file. This provides the basic results from Kraken2 but with the corrected abundance information.
 
 ### Kraken2
 
@@ -256,10 +258,11 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `
 <summary>Output files</summary>
 
 - `centrifuge`
-  - `<sample_id>.centrifuge.mapped.fastq.gz`
+  - `<sample_id>.centrifuge.mapped.fastq.gz`: Fastq files containing all mapped reads
-  - `<sample_id>.centrifuge.report.txt`
+  - `<sample_id>.centrifuge.report.txt`: A classification report that summarises the taxonomic ID, the taxonomic rank, length of genome sequence, number of classified and uniquely classified reads
-  - `<sample_id>.centrifuge.results.txt`
+  - `<sample_id>.centrifuge.results.txt`: A file that summarises the classification assignment for a read, i.e read ID, sequence ID, score for the classification, score for the next best classification, number of classifications for this read
-  - `<sample_id>.centrifuge.unmapped.fastq.gz`
+  - `<sample_id>.centrifuge.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of k-mers, taxonomic path of all the hits in the centrifuge run for a given sample
+  - `<sample_id>.centrifuge.unmapped.fastq.gz`: Fastq file containing all unmapped reads
 
 </details>
 
@@ -269,7 +272,8 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `
 <summary>Output files</summary>
 
 - `kaiju`
-  - `<sample_id>.tsv`
+  - `<sample_id>.tsv`: A file that summarises the fraction abundance, taxonomic ID, number of reads and taxonomic names
+  - `kaiju_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `kaiju2table`)
 
 </details>
 
@@ -279,8 +283,8 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `
 <summary>Output files</summary>
 
 - `diamond`
-  - `<sample_id>.log`
+  - `<sample_id>.log`: A log file containing stdout information
-  - `<sample_id>.sam`
+  - `<sample_id>.sam`: A file in SAM format that contains the aligned reads
 
 </details>
 
@@ -321,22 +325,23 @@ You will only recieve the `.sam` and `.megan` files if you supply `--malt_save_r
 
 </details>
 
-The main taxonomic profiling file from MetaPhlAn3 is the `*_profile.txt` file. This provides the abundance estimates from MetaPhlAn3 however does not include raw counts by default. 
+The main taxonomic profiling file from MetaPhlAn3 is the `*_profile.txt` file. This provides the abundance estimates from MetaPhlAn3 however does not include raw counts by default.
 ### mOTUs
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `motus`
-  - `<sample_id>.log`
+  - `<sample_id>.log`: A log file that contains summary statistics
-  - `<sample_id>.out`
+  - `<sample_id>.out`: A classification file that summarises taxonomic identifiers, by default at the rank of mOTUs (i.e., species level), and their relative abundances in the profiled sample.
+  - `motus_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `motus_merge`)
 
 </details>
 ### Krona
 
 [Krona](https://github.com/marbl/Krona) is Krona allows the exploration of (metagenomic) hierarchical data with interactive zooming, multi-layered pie charts.
 
-Krona charts will be generated by the pipeline for supported tools (Kraken2, Centrifuge, Kaiju, and MALT) 
+Krona charts will be generated by the pipeline for supported tools (Kraken2, Centrifuge, Kaiju, and MALT)
 
 <details markdown="1">
 <summary>Output files</summary>