Merge branch 'dev' into json-schema

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/taxp
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/taxprofiler/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/taxprofiler/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/taxprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-  - [ ] If necessary, also make a PR on the nf-core/taxprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/ci.yml

@@ -10,7 +10,6 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  CAPSULE_LOG: none
 
 jobs:
   test:
@@ -20,14 +19,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Nextflow versions
+        NXF_VER:
-        include:
+          - "21.10.3"
-          # Test pipeline minimum Nextflow version
+          - "latest-everything"
-          - NXF_VER: "21.10.3"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
         parameters:
           - "--perform_longread_qc false"
           - "--perform_shortread_qc false"
@@ -48,14 +42,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
+        uses: nf-core/setup-nextflow@v1
-          NXF_VER: ${{ matrix.NXF_VER }}
+        with:
-          # Uncomment only if the edge release is more recent than the latest stable release
+          version: "${{ matrix.NXF_VER }}"
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
 
       - name: Show current locale
         run: locale

.github/workflows/linting.yml

@@ -35,6 +35,36 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Check code lints with Black
+        uses: psf/black@stable
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
@@ -42,15 +72,11 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
+        uses: nf-core/setup-nextflow@v1
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
 
       - uses: actions/setup-python@v3
         with:
-          python-version: "3.6"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies

.prettierignore

@@ -6,5 +6,5 @@ results/
 .DS_Store
 testing/
 testing*
-tests/
 *.pyc
+tests/

CITATION.cff

@@ -0,0 +1,56 @@
+cff-version: 1.2.0
+message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
+authors:
+  - family-names: Ewels
+    given-names: Philip
+  - family-names: Peltzer
+    given-names: Alexander
+  - family-names: Fillinger
+    given-names: Sven
+  - family-names: Patel
+    given-names: Harshil
+  - family-names: Alneberg
+    given-names: Johannes
+  - family-names: Wilm
+    given-names: Andreas
+  - family-names: Ulysse Garcia
+    given-names: Maxime
+  - family-names: Di Tommaso
+    given-names: Paolo
+  - family-names: Nahnsen
+    given-names: Sven
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+  type: article
+  authors:
+    - family-names: Ewels
+      given-names: Philip
+    - family-names: Peltzer
+      given-names: Alexander
+    - family-names: Fillinger
+      given-names: Sven
+    - family-names: Patel
+      given-names: Harshil
+    - family-names: Alneberg
+      given-names: Johannes
+    - family-names: Wilm
+      given-names: Andreas
+    - family-names: Ulysse Garcia
+      given-names: Maxime
+    - family-names: Di Tommaso
+      given-names: Paolo
+    - family-names: Nahnsen
+      given-names: Sven
+  doi: 10.1038/s41587-020-0439-x
+  journal: nature biotechnology
+  start: 276
+  end: 278
+  title: "The nf-core framework for community-curated bioinformatics pipelines."
+  issue: 3
+  volume: 38
+  year: 2020
+  url: https://dx.doi.org/10.1038/s41587-020-0439-x

README.md

@@ -1,19 +1,14 @@
 # ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_dark.png#gh-dark-mode-only)
 
-[![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+CI%22)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
-[![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/)
+[![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?logo=docker)](https://www.docker.com/)
+[![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)](https://sylabs.io/docs/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/taxprofiler)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?logo=slack)](https://nfcore.slack.com/channels/taxprofiler)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)[![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)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
-[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -59,7 +54,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-   ```console
+   ```bash
    nextflow run nf-core/taxprofiler -profile test,YOURPROFILE --outdir <OUTDIR>
    ```
 

assets/email_template.txt

@@ -6,7 +6,6 @@
                                         `._,._,'
   nf-core/taxprofiler v${version}
 ----------------------------------------------------
-
 Run Name: $runName
 
 <% if (success){

bin/check_samplesheet.py

@@ -6,7 +6,6 @@ import sys
 import errno
 import argparse
 
-
 def parse_args(args=None):
     Description = (
         "Reformat nf-core/taxprofiler samplesheet file and check its contents."
@@ -18,7 +17,6 @@ def parse_args(args=None):
     parser.add_argument("FILE_OUT", help="Output file.")
     return parser.parse_args(args)
 
-
 def make_dir(path):
     if len(path) > 0:
         try:
@@ -27,7 +25,6 @@ def make_dir(path):
             if exception.errno != errno.EEXIST:
                 raise exception
 
-
 def print_error(error, context="Line", context_str=""):
     error_str = "ERROR: Please check samplesheet -> {}".format(error)
     if context != "" and context_str != "":
@@ -37,7 +34,6 @@ def print_error(error, context="Line", context_str=""):
     print(error_str)
     sys.exit(1)
 
-
 def check_samplesheet(file_in, file_out):
     """
     This function checks that the samplesheet follows the following structure:

conf/base.config

@@ -26,6 +26,11 @@ process {
     //        adding in your local modules too.
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+    withLabel:process_single {
+        cpus   = { check_max( 1                  , 'cpus'    ) }
+        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+    }
     withLabel:process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
         memory = { check_max( 12.GB * task.attempt, 'memory'  ) }

docs/usage.md

@@ -154,7 +154,7 @@ This will launch the pipeline with the `docker` configuration profile. See below
 
 Note that the pipeline will create the following files in your working directory:
 
-```console
+```bash
 work                # Directory containing the nextflow working files
 <OUTDIR>            # Finished results in specified location (defined with --outdir)
 .nextflow_log       # Log file from Nextflow
@@ -231,7 +231,7 @@ nf-core/taxprofiler uses MALT 0.4.1, which is a compatively old version. However
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
-```console
+```bash
 nextflow pull nf-core/taxprofiler
 ```
 
@@ -407,6 +407,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
 We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
 
-```console
+```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```

lib/WorkflowMain.groovy

@@ -59,6 +59,7 @@ class WorkflowMain {
         }
 
         // Print parameter summary log to screen
+
         log.info paramsSummaryLog(workflow, params, log)
 
         // Check that a -profile or Nextflow config has been provided to run the pipeline
@@ -78,17 +79,15 @@ class WorkflowMain {
             System.exit(1)
         }
     }
-
     //
     // Get attribute from genome config file e.g. fasta
     //
-    public static String getGenomeAttribute(params, attribute) {
+    public static Object getGenomeAttribute(params, attribute) {
-        def val = ''
         if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
             if (params.genomes[ params.genome ].containsKey(attribute)) {
-                val = params.genomes[ params.genome ][ attribute ]
+                return params.genomes[ params.genome ][ attribute ]
             }
         }
-        return val
+        return null
     }
 }

lib/WorkflowTaxprofiler.groovy

@@ -42,9 +42,7 @@ class WorkflowTaxprofiler {
         yaml_file_text        += "data: |\n"
         yaml_file_text        += "${summary_section}"
         return yaml_file_text
-    }
+    }//
-
-    //
     // Exit pipeline if incorrect --genome key provided
     //
     private static void genomeExistsError(params, log) {

modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -1,9 +1,10 @@
 #!/usr/bin/env python
 
-import yaml
 import platform
 from textwrap import dedent
 
+import yaml
+
 
 def _make_versions_html(versions):
     html = [
@@ -58,7 +59,8 @@ versions_by_module = {}
 for process, process_versions in versions_by_process.items():
     module = process.split(":")[-1]
     try:
-        assert versions_by_module[module] == process_versions, (
+        if versions_by_module[module] != process_versions:
+            raise AssertionError(
                 "We assume that software versions are the same between all modules. "
                 "If you see this error-message it means you discovered an edge-case "
                 "and should open an issue in nf-core/tools. "

nextflow.config

@@ -13,11 +13,11 @@ params {
     // Input options
     input                      = null
 
+
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
-
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -37,6 +37,7 @@ params {
     schema_ignore_params       = 'genomes,fasta'
     enable_conda               = false
 
+
     // Config options
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
@@ -45,6 +46,7 @@ params {
     config_profile_url         = null
     config_profile_name        = null
 
+
     // Max resource options
     // Defaults only, expecting to be overwritten
     max_memory                 = '128.GB'
@@ -157,6 +159,7 @@ try {
 }
 
 
+
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
@@ -167,6 +170,15 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
     }
+    mamba {
+        params.enable_conda    = true
+        conda.useMamba         = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
     docker {
         docker.enabled         = true
         docker.userEmulation   = true
@@ -204,6 +216,11 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
     }
+    gitpod {
+        executor.name          = 'local'
+        executor.cpus          = 16
+        executor.memory        = 60.GB
+    }
     test                    { includeConfig 'conf/test.config'      }
     test_full               { includeConfig 'conf/test_full.config' }
     test_noprofiling        { includeConfig 'conf/test_noprofiling.config' }
@@ -212,6 +229,7 @@ profiles {
     test_motus              { includeConfig 'conf/test_motus.config' }
 }
 
+
 // Load igenomes.config if required
 
 if (!params.igenomes_ignore) {
@@ -220,6 +238,7 @@ if (!params.igenomes_ignore) {
     params.genomes = [:]
 }
 
+
 // 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.
 // 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.