credits update

README.md

@@ -96,3 +96,22 @@ nextflow run maxibor/organdiet --help
 # An example workflow for this pipeline
 
 ![](./img/flowchart.png)
+
+# Credits
+
+The OrganDiet pipeline uses many tools listed below:
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [AdapterRemoval](https://github.com/MikkelSchubert/adapterremoval)
+- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
+- [Samtools](http://www.htslib.org/)
+- [Diamond](https://github.com/bbuchfink/diamond)
+- [Centrifuge](https://ccb.jhu.edu/software/centrifuge/manual.shtml)
+- [BASTA](https://github.com/timkahlke/BASTA)
+- [ReCentrifuge](https://github.com/khyox/recentrifuge)
+- [Krona](https://github.com/marbl/Krona/wiki)
+- [Nextflow](https://www.nextflow.io/)
+
+The author of OrganDiet also got some inspiration and help from the following awesome developers:
+- [Paolo Di Tomasso](https://twitter.com/paoloditommaso)
+- [Phil Ewels](https://twitter.com/tallphil)
+- [Tim Kahlke](https://twitter.com/AdvancedTwigTec)

main.nf

@@ -18,8 +18,6 @@ Pipeline overview:
  - 3:   Build Bowtie DB of control. If control provided.
  - 4:   Align on control, output unaligned reads. If control provided.
  - 5:   Align on human genome, output unaligned reads
- - 4:   Picard for duplicate read identification
- - 5:   Statistics about read counts
  - 6:   Align on organellome database
  - 7:   Extract Mapped reads
  - 8:   Filter reads on quality and length