Merge branch 'dev' into modules_update

nf-core · Oct 2, 2023 · 5e7cc6b · 5e7cc6b
2 parents 7228cd9 + 6cdd651
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/funcscan then the best place to ask is on the nf-core Slack [#funcscan](https://nfcore.slack.com/channels/funcscan) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/funcscan then the best place to ask is on the nf-core Slack [#funcscan](https://nfcore.slack.com/channels/funcscan) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml
@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/bluesky-post-action@v0.0.2
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#306](https://github.com/nf-core/funcscan/pull/306) Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
 - [#307](https://github.com/nf-core/funcscan/pull/307) Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133)
 
 ### `Dependencies`

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
diff --git a/README.md b/README.md
@@ -1,6 +1,8 @@
 # ![nf-core/funscan](docs/images/nf-core-funcscan_logo_flat_light.png#gh-light-mode-only) ![nf-core/funscan](docs/images/nf-core-funcscan_logo_flat_dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7643099-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7643099)
+[![GitHub Actions CI Status](https://github.com/nf-core/funcscan/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/funcscan/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/nf-core/funcscan/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/funcscan/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/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7643099-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7643099)
+
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](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/)
@@ -33,10 +35,11 @@ The nf-core/funcscan AWS full test dataset are contigs generated by the MGnify s
 
 ## Usage
 
-> **Note**
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-> with `-profile test` before running the workflow on actual data.
+:::note
+If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+with `-profile test` before running the workflow on actual data.
+:::
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -63,10 +66,11 @@ nextflow run nf-core/funcscan \
    --run_bgc_screening
 ```
 
-> **Warning:**
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::warning
+Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/funcscan/1.1.4dev" target="_blank">nf-core/funcscan</a>
+  This report has been generated by the <a href="https://github.com/nf-core/funcscan/releases/tag/dev" target="_blank">nf-core/funcscan</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/funcscan/1.1.4dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/funcscan/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-funcscan-methods-description":
     order: -1000

diff --git a/conf/modules.config b/conf/modules.config
@@ -65,8 +65,7 @@ process {
             "--mincontiglen ${params.annotation_prokka_mincontiglen}",
             "--evalue ${params.annotation_prokka_evalue}",
             "--coverage ${params.annotation_prokka_coverage}",
-            "--centre ${params.annotation_prokka_centre}",
-            "--locustag ${params.annotation_prokka_locustag}",
+            params.annotation_prokka_retaincontigheaders ? "--force" : "--locustag PROKKA --centre CENTER" ,
             params.annotation_prokka_singlemode ? '' : '--metagenome' ,
             params.annotation_prokka_cdsrnaolap ? '--cdsrnaolap' : '',
             params.annotation_prokka_rawproduct ? '--rawproduct' : '',

diff --git a/docs/output.md b/docs/output.md
@@ -575,6 +575,7 @@ Output Summaries:
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+  - Parameters used by the pipeline run: `params.json`.
 
 </details>
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -249,7 +249,9 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::warning
+Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -286,19 +288,25 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducibility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::tip
+If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::
 
 ## Core Nextflow arguments
 
-> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::note
+These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::
 
 ### `-profile`
 
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::info
+We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::
 
 The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 

diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
@@ -3,6 +3,7 @@
 //
 
 import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
 
 class NfcoreTemplate {
 
@@ -222,6 +223,21 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Dump pipeline parameters in a json file
+    //
+    public static void dump_parameters(workflow, params) {
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+
+        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def jsonStr    = JsonOutput.toJson(params)
+        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    }
+
     //
     // Print pipeline summary on completion
     //

diff --git a/lib/WorkflowFuncscan.groovy b/lib/WorkflowFuncscan.groovy
@@ -52,6 +52,8 @@ class WorkflowFuncscan {
 
     public static String toolCitationText(params) {
 
+        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
+        // Uncomment function in methodsDescriptionText to render in MultiQC report
         def preprocessing_text = "The pipeline used the following tools: preprocessing included bioawk (Li 2023)."
 
         def annotation_text    = [

diff --git a/nextflow.config b/nextflow.config
@@ -62,10 +62,9 @@ params {
     annotation_prokka_mincontiglen          = 1
     annotation_prokka_evalue                = 1E-06
     annotation_prokka_coverage              = 80
-    annotation_prokka_centre                = null
-    annotation_prokka_compliant             = false
-    annotation_prokka_locustag              = 'PROKKA'
+    annotation_prokka_compliant             = true
     annotation_prokka_addgenes              = false
+    annotation_prokka_retaincontigheaders   = false
 
     // Database downloading options
     save_databases                          = false
@@ -211,7 +210,7 @@ params {
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes'
+    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
     validationShowHiddenParams       = false
     validate_params                  = true
 
@@ -313,6 +312,7 @@ profiles {
     }
     apptainer {
         apptainer.enabled      = true
+        apptainer.autoMounts   = true
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -322,8 +322,8 @@ profiles {
     }
     gitpod {
         executor.name          = 'local'
-        executor.cpus          = 16
-        executor.memory        = 60.GB
+        executor.cpus          = 4
+        executor.memory        = 8.GB
     }
     test         { includeConfig 'conf/test.config'         }
     test_bgc     { includeConfig 'conf/test_bgc.config'     }

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -297,30 +297,22 @@
                     "help_text": "Activates [RNAmmer](https://services.healthtech.dtu.dk/service.php?RNAmmer-1.2) instead of the Prokka default [Barrnap](https://github.com/tseemann/barrnap) for rRNA prediction during the annotation process. RNAmmer classifies ribosomal RNA genes in genome sequences by using two levels of Hidden Markov Models. Barrnap uses the nhmmer tool that includes HMMER 3.1 for HMM searching in RNA:DNA style.\n\nFor more information please check Prokka [documentation](https://github.com/tseemann/prokka).\n\n> Modifies tool parameter(s):\n> - Prokka: `--rnammer`",
                     "fa_icon": "fas fa-adjust"
                 },
-                "annotation_prokka_centre": {
-                    "type": "string",
-                    "description": "Sequencing centre ID.",
-                    "fa_icon": "fas fa-map-marker-alt",
-                    "help_text": "Add the sequencing center ID used in generating the raw sequences. This flag is typically requested in combination with the `--compliant` flag when contigs need to be renamed due to non-conforming contig headers. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--centre`"
-                },
                 "annotation_prokka_compliant": {
                     "type": "boolean",
                     "fa_icon": "far fa-check-circle",
                     "description": "Force contig name to Genbank/ENA/DDJB naming rules.",
                     "help_text": "Force the contig headers to conform to the Genbank/ENA/DDJB contig header standards. This is activated in combination with `--centre [X]` when contig headers supplied by the user are non-conforming and therefore need to be renamed before Prokka can start annotation. This flag activates  `--genes --mincontiglen 200`. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--compliant`"
                 },
-                "annotation_prokka_locustag": {
-                    "type": "string",
-                    "default": "Prokka",
-                    "fa_icon": "fas fa-tags",
-                    "description": "Assign the locus tag for the contig header.",
-                    "help_text": "Assign a special name to the contig. This is used when a specific group of samples are run in a batch. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--locustag`"
-                },
                 "annotation_prokka_addgenes": {
                     "type": "boolean",
                     "fa_icon": "fas fa-dna",
                     "description": "Add the gene features for each CDS hit.",
                     "help_text": "For every CDS annotated, this flag adds the gene that encodes for that CDS region. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--addgenes`"
+                },
+                "annotation_prokka_retaincontigheaders": {
+                    "type": "boolean",
+                    "help_text": "This parameter allows prokka to retain the original contig names by activating `PROKKA`'s  `--force` flag. If this parameter is set to `false` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. By default `PROKKA` changes contig headers to avoid errors that might rise due to long contig headers, so this must be turned on if the user has short contig names that should be retained by `PROKKA`. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`",
+                    "description": "Retains contig names."
                 }
             },
             "fa_icon": "fas fa-tools",
@@ -1129,14 +1121,6 @@
                     "fa_icon": "far fa-file-code",
                     "hidden": true
                 },
-                "igenomes_base": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes",
-                    "fa_icon": "fas fa-cloud-download-alt",
-                    "hidden": true
-                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",