github-handle

.gitignore

@@ -6,3 +6,5 @@ ont
 *.simg
 .nextflow.log*
 .nextflow/*
+data
+SRR12*

README.md

@@ -25,3 +25,4 @@ a summary (QUAST for assemblys statistics, MultiQC report).
 
 * [Learning Nextflow in 2020](https://www.nextflow.io/blog/2020/learning-nextflow-in-2020.html), blog post by Evan Floden & Alain Coletta
 * [nf-core community](https://nf-co.re/), a set of high quality bioinformatics pipeline backed by a fantastic community
+* [Video: introduction to MultiQC](https://www.youtube.com/watch?v=BbScv9TcaMg&ab_channel=PhilEwels)

assembly_1.nf

@@ -28,7 +28,7 @@ reads = Channel
 
 // prints to the screen and to the log
 log.info """
-         RNAquant Pipeline
+         Denovo Pipeline
          ===================================
          reads        : ${params.reads}
          outdir       : ${params.outdir}

assembly_2.nf

@@ -2,10 +2,11 @@
  *   An assembly pipeline in Nextflow DSL2
  *   -----------------------------------------
 
- This version adds support for Prokka in the MultiQC
- pipeline. This requires a change in the MultiQC step
- to force the use of Prokka filename as sample ID
- (otherwise MultiQC uses the Genus/Species from Prokka) 
+ == V2 ==
+ This version collects the results from the assembly
+ to make the Quast report.
+ Moreover collects the results from Quast and Fastp
+ to generate a MultiQC report.
 
 
  */
@@ -29,7 +30,7 @@ reads = Channel
 
 // prints to the screen and to the log
 log.info """
-         RNAquant Pipeline
+         Denovo Pipeline
          ===================================
          reads        : ${params.reads}
          outdir       : ${params.outdir}

assembly_3.nf

@@ -30,7 +30,7 @@ reads = Channel
 
 // prints to the screen and to the log
 log.info """
-         RNAquant Pipeline
+         Denovo Pipeline
          ===================================
          reads        : ${params.reads}
          outdir       : ${params.outdir}

getdata.sh

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+if [[ ! -e "imgs" ]]; then
+    echo "This script should be executed from the repository root."
+    exit 1
+fi
+set -euxo pipefail
+mkdir -p data
+
+curl --silent -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR128/099/SRR12825099/SRR12825099_1.fastq.gz -o data/SRR12825099_Shigella_R1.fastq.gz
+curl --silent -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR128/099/SRR12825099/SRR12825099_2.fastq.gz -o data/SRR12825099_Shigella_R2.fastq.gz
+curl --silent -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR129/042/SRR12971242/SRR12971242_1.fastq.gz -o data/SRR12971242_Escherichia_R1.fastq.gz
+curl --silent -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR129/042/SRR12971242/SRR12971242_2.fastq.gz -o data/SRR12971242_Escherichia_R2.fastq.gz
+curl --silent -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR129/041/SRR12971241/SRR12971241_1.fastq.gz -o data/SRR12971241_Escherichia_R1.fastq.gz
+curl --silent -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR129/041/SRR12971241/SRR12971241_2.fastq.gz -o data/SRR12971241_Escherichia_R2.fastq.gz

assembly_dev.nf → main.nf

@@ -16,7 +16,7 @@ reads = Channel
 
 // prints to the screen and to the log
 log.info """
-         RNAquant Pipeline
+         Denovo Pipeline
          ===================================
          reads        : ${params.reads}
          outdir       : ${params.outdir}
@@ -151,8 +151,7 @@ process multiqc {
     """
 } 
 
-workflow {
-
+workflow {    
     fastp( reads )
     assembly( fastp.out.reads )
     prokka( assembly.out )