update description and README

README.md

@@ -3,7 +3,7 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/bacass/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/bacass/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bacass/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2669428-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2669428)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -16,8 +16,7 @@
 
 ## Introduction
 
-<!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
-**nf-core/bacass** is a bioinformatics best-practice analysis pipeline for Simple bacterial assembly and annotation pipeline..
+**nf-core/bacass** is a bioinformatics best-practice analysis pipeline for simple bacterial assembly and annotation. The pipeline is able to assemble short reads, long reads, or a mixture of short and long reads (hybrid assembly).
 
 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!
 
@@ -26,10 +25,18 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+### Short Read Assembly
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using [Skewer](https://github.com/relipmoc/skewer) and performs basic sequencing QC using [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, the pipeline performs read assembly using [Unicycler](https://github.com/rrwick/Unicycler). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) to verify sample purity.
+
+### Long Read Assembly
+
+For users that only have Nanopore data, the pipeline quality trims these using [PoreChop](https://github.com/rrwick/Porechop) and assesses basic sequencing QC utilizing [NanoPlot](https://github.com/wdecoster/NanoPlot) and [PycoQC](https://github.com/a-slide/pycoQC).
+The pipeline can then perform long read assembly utilizing [Unicycler](https://github.com/rrwick/Unicycler), [Miniasm](https://github.com/lh3/miniasm) in combination with [Racon](https://github.com/isovic/racon) or [Canu](https://github.com/marbl/canu). Long reads can be polished using specified Fast5 files with [NanoPolish](https://github.com/jts/nanopolish).
+
+### Hybrid Assembly
+
+For users specifying both short read and long read (NanoPore) data, the pipeline can perform a hybrid assembly approach utilizing [Unicycler](https://github.com/rrwick/Unicycler), taking the full set of information from short reads and long reads into account.
 
 ## Quick Start
 
@@ -75,8 +82,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  nf-core/bacass for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use  nf-core/bacass for your analysis, please cite it using the following doi: [10.5281/zenodo.2669428](https://doi.org/10.5281/zenodo.2669428)
 
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

assets/email_template.html

@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/bacass: Simple bacterial assembly and annotation pipeline.">
+  <meta name="description" content="nf-core/bacass: Simple bacterial assembly and annotation">
   <title>nf-core/bacass Pipeline Report</title>
 </head>
 <body>

modules/local/abc.nf

@@ -0,0 +1,50 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process DADA2_FILTNTRIM {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? "bioconductor-dada2=1.18.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.18.0--r40h5f743cb_0"
+    } else {
+        container "quay.io/biocontainers/bioconductor-dada2:1.18.0--r40h5f743cb_0"
+    }
+
+    input:
+    tuple val(meta), path(reads), val(trunclenf), val(trunclenr)
+
+    output:
+    tuple val(meta), path("*.filter_stats.tsv"), emit: log
+    tuple val(meta), path("*.filt.fastq.gz")   , emit: reads
+    path "*.version.txt"                       , emit: version
+    path "*.args.txt"                          , emit: args
+
+    script:
+    def software    = getSoftwareName(task.process)
+    def in_and_out  = meta.single_end ? "\"${reads}\", \"${meta.id}.filt.fastq.gz\"" : "\"${reads[0]}\", \"${meta.id}_1.filt.fastq.gz\", \"${reads[1]}\", \"${meta.id}_2.filt.fastq.gz\""
+    def trunclenf   = trunclenf[1].toInteger()
+    def trunclenr   = trunclenr[1].toInteger()
+    def trunc_args  = meta.single_end ? "truncLen = $trunclenf" : "truncLen = c($trunclenf, $trunclenr)"
+    """
+    #!/usr/bin/env Rscript
+    suppressPackageStartupMessages(library(dada2))
+    out <- filterAndTrim($in_and_out,
+        $trunc_args,
+        $options.args,
+        compress = TRUE,
+        multithread = $task.cpus,
+        verbose = TRUE)
+    out <- cbind(out, ID = row.names(out))
+    write.table( out, file = "${meta.id}.filter_stats.tsv", sep = "\t", row.names = FALSE, quote = FALSE)
+    write.table(paste('filterAndTrim\t$trunc_args','$options.args',sep=","), file = "filterAndTrim.args.txt", row.names = FALSE, col.names = FALSE, quote = FALSE)
+    write.table(packageVersion("dada2"), file = "${software}.version.txt", row.names = FALSE, col.names = FALSE, quote = FALSE)
+    """
+}

nextflow.config

@@ -158,7 +158,7 @@ manifest {
     name            = 'nf-core/bacass'
     author          = 'Andreas Wilm, Alexander Peltzer'
     homePage        = 'https://github.com/nf-core/bacass'
-    description     = 'Simple bacterial assembly and annotation pipeline.'
+    description     = 'Simple bacterial assembly and annotation'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
     version         = '1.1.1'

nextflow_schema.json

@@ -2,7 +2,7 @@
     "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/bacass/master/nextflow_schema.json",
     "title": "nf-core/bacass pipeline parameters",
-    "description": "Simple bacterial assembly and annotation pipeline.",
+    "description": "Simple bacterial assembly and annotation",
     "type": "object",
     "definitions": {
         "input_output_options": {