Prepare release 2.0.0

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.10.0', '']
+        nxf_ver: ['21.04.0', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -46,7 +46,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.10.0'
+      NXF_VER: '21.04.0'
       NXF_ANSI_LOG: false
     strategy:
       matrix:

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.3.0dev - [date]
+## v2.0.0 - 2021/05/26
 
 ### `Added`
 
@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#178](https://github.com/nf-core/mag/pull/178) - Change output file: `results/GenomeBinning/QC/quast_and_busco_summary.tsv` -> `results/GenomeBinning/bin_summary.tsv`, contains GTDB-Tk results as well.
 - [#191](https://github.com/nf-core/mag/pull/191) - Update to nf-core 1.14 `TEMPLATE`
 - [#193](https://github.com/nf-core/mag/pull/193) - Compress CAT output files [#180](https://github.com/nf-core/mag/issues/180)
+- [#198](https://github.com/nf-core/mag/pull/198) - Requires nextflow version `>= 21.04.0`
 
 ### `Fixed`
 
@@ -35,7 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#195](https://github.com/nf-core/mag/pull/195) - Fix documentation regarding required compression of input FastQ files [#160](https://github.com/nf-core/mag/issues/160)
 - [#196](https://github.com/nf-core/mag/pull/196) - Add process for CAT database creation as solution for problem caused by incompatible `DIAMOND` version used for pre-built `CAT database` and `CAT classification` [#90](https://github.com/nf-core/mag/issues/90), [#188](https://github.com/nf-core/mag/issues/188)
 
-## v1.2.0 - 2020/02/10
+## v1.2.0 - 2021/02/10
 
 ### `Added`
 

README.md

@@ -4,12 +4,17 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/mag/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/mag/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/mag/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mag/actions)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.10.0-brightgreen.svg)](https://www.nextflow.io/)
-
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
-[![Docker](https://img.shields.io/docker/automated/nfcore/mag.svg)](https://hub.docker.com/r/nfcore/mag)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3589527.svg)](https://doi.org/10.5281/zenodo.3589527)
+
+[![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/)
+[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?logo=slack)](https://nfcore.slack.com/channels/mag)
+[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)
+[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -23,7 +28,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Quick Start
 
-1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.04.0`)
+1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=21.04.0`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 

nextflow.config

@@ -231,8 +231,8 @@ manifest {
   homePage = 'https://github.com/nf-core/mag'
   description = 'Assembly, binning and annotation of metagenomes'
   mainScript = 'main.nf'
-  nextflowVersion = '>=20.10.0'
-  version = '1.3.0dev'
+  nextflowVersion = '!>=21.04.0'
+  version = '2.0.0'
 }
 
 // Function to ensure that resource requirements don't go beyond

nextflow_schema.json

@@ -390,12 +390,12 @@
                 "centrifuge_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with centrifuge.",
-                    "help_text": "E.g. \"ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz\"."
+                    "help_text": "E.g. ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz."
                 },
                 "kraken2_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with kraken2.",
-                    "help_text": "The database file must be a compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. \"ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz\"."
+                    "help_text": "The database file must be a compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz."
                 },
                 "skip_krona": {
                     "type": "boolean",
@@ -404,16 +404,16 @@
                 "cat_db": {
                     "type": "string",
                     "description": "Database for taxonomic classification of metagenome assembled genomes.",
-                    "help_text": "E.g. \"https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz\".\nThe zipped file needs to contain a folder named \"*taxonomy*\" and \"*CAT_database*\" that hold the respective files."
+                    "help_text": "E.g. https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz. This parameter is mutually exclusive with `--cat_db_generate`. The zipped file needs to contain a folder named `*taxonomy*` and `*database*` that hold the respective files."
                 },
                 "cat_db_generate": {
                     "type": "boolean",
                     "description": "Generate CAT database.",
-                    "help_text": "Download the taxonomy files from NCBI taxonomy, the nr database and generate CAT database. Useful to build a CAT database with the same DIAMOND version as used for running CAT classification, avoiding compatibility problems."
+                    "help_text": "Download the taxonomy files from NCBI taxonomy, the nr database and generate CAT database. This parameter is mutually exclusive with `--cat_db`. Useful to build a CAT database with the same DIAMOND version as used for running CAT classification, avoiding compatibility problems."
                 },
                 "save_cat_db": {
                     "type": "boolean",
-                    "description": "Save the CAT database generated when specified by --cat_db_generate.",
+                    "description": "Save the CAT database generated when specified by `--cat_db_generate`.",
                     "help_text": "Useful to allow reproducibility, as old versions of prebuild CAT databases do not always remain accessible and underlying NCBI taxonomy and nr databases change."
                 },
                 "gtdb": {