From 7321daf4f6f141efae218a34b2b69c482d1dfeed Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 18 Feb 2022 08:41:34 +0100
Subject: [PATCH 1/2] Update README with approximate pipeline outline

---
 README.md | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 8f33f2c..f57666d 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@
 ## Introduction
 
 <!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
-**nf-core/taxprofiler** is a bioinformatics best-practice analysis pipeline for Taxonomic profiling of shotgun metagenomic data.
+**nf-core/taxprofiler** is a bioinformatics best-practice analysis pipeline for taxonomic profiling of shotgun metagenomic data. It allows for in-parallel profiling against multiple profiling tools and databases and produces standardised output tables.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
@@ -29,7 +29,23 @@ On release, automated continuous integration tests run the pipeline on a full-si
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+2. Performs optional read pre-processing
+   - Adapter clipping and merging
+   - Low complexity filtering
+   - Host read removal
+   - Run merging
+3. Performs taxonomic profiling a choice of:
+   - Kraken2
+   - MetaPhlAn3
+   - MALT
+   - DIAMOND
+   - Centrifuge
+   - Kaiju
+   - mOTUs
+4.  Perform optional post-processing with:
+    -  bracken
+5.  Standardises output tables
+6. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Quick Start
 

From c68afbbf90c98e87716dc526d6c5a9631a341201 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 18 Feb 2022 08:45:06 +0100
Subject: [PATCH 2/2] Update nextflow.config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index c2d51b5..186979c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -121,7 +121,7 @@ if (!params.igenomes_ignore) {
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
-// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. 
+// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
 
 env {