Adding images of outputs to output.md

docs/output.md

@@ -61,6 +61,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
+![BLAZE - knee plot](images/blaze.png)
+
 [BLAZE](https://github.com/shimlab/BLAZE) enables the accurate identification of barcodes and UMIs from Nanopore reads.
 
 ## Alignment
@@ -108,6 +110,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
         - `*.dedup.stats`
 </details>
 
+![MultiQC - samtools idxstats](images/samtools_idxstats.png)
+![MultiQC - samtools stats](images/samtools_stats.png)
+
 [Samtools](https://www.htslib.org/) is a suite of programs for reading, writing, editing, indexing, and viewing files that are in SAM, BAM, or CRAM format
 
 ### Barcode Correction
@@ -136,6 +141,8 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 </details>
 
+![MultiQC - umitools dedup](images/umitools_dedup.png)
+
 [UMI-Tools](https://umi-tools.readthedocs.io/en/latest/reference/dedup.html) deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. The identification of duplicate reads is performed in an error-aware manner by building networks of related UMIs 
 
 ## Feature-Barcode Quantification
@@ -166,6 +173,8 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
       - `*.png`
 </details>
 
+![MultiQC - seurat](images/samtools_idxstats.png)
+
 [Seurat](https://satijalab.org/seurat/) is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 
 
 ## Quality Control
@@ -240,6 +249,9 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 </details>
 
+![Nanocomp](images/nanocomp_1.png)
+![Nanocomp](images/nanocomp_2.png)
+
 [Nanocomp](https://github.com/wdecoster/nanocomp) compares multiple runs of long read sequencing data and alignments. It creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot
 
 ### Nanoplot
@@ -289,8 +301,27 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 </details>
 
+![Nanoplot](images/nanoplot_1.png)
+![Nanoplot](images/nanoplot_2.png)
+
 [Nanoplot](https://github.com/wdecoster/NanoPlot) is a plotting tool for long read sequencing data and alignments.
 
+### RSeQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `<sample_identifier>/`
+  - `qc/`
+    - `rseqc/`
+      - `*.read_distribution.txt`
+
+</details>
+
+![RSeQC](images/rseqc.png)
+
+[RSeQC](https://rseqc.sourceforge.net/) package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data
+
 ### MultiQC
 
 <details markdown="1">