Merge pull request #38 from genomic-medicine-sweden/template_2.10

Template 2.10

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.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 tomte then the best way to ask is by creating an [issue] (https://github.com/genomic-medicine-sweden/tomte/issues).
+:::info
+If you need help using or modifying genomic-medicine-sweden/tomte then the best place to ask is by creating an [issue] (https://github.com/genomic-medicine-sweden/tomte/issues).
+:::
 
 ## Contribution workflow
 

.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

CITATIONS.md

@@ -28,7 +28,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [GATK](https://genome.cshlp.org/content/20/9/1297)
 

README.md

@@ -1,14 +1,15 @@
 # ![tomte](docs/images/tomte_logo_light.png#gh-light-mode-only) ![tomte](docs/images/tomte_logo_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/tomte/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 CI Status](https://github.com/genomic-medicine-sweden/tomte/workflows/nf-core%20CI/badge.svg)](https://github.com/genomic-medicine-sweden/tomte/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/tomte/workflows/nf-core%20linting/badge.svg)](https://github.com/genomic-medicine-sweden/tomte/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/tomte/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![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/)
 [![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/)
-[![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/tomte)
+[![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/genomic-medicine-sweden/tomte)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23tomte-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/tomte)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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
 
@@ -31,10 +32,11 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## 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:
 
@@ -58,17 +60,17 @@ nextflow run genomic-medicine-sweden/tomte \
    --outdir <OUTDIR>
 ```
 
-> **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, please refer to the [usage documentation](https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/usage.md) and the [parameter documentation](https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/parameters.md).
+For more details and further functionality, please refer to the [usage documentation](https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/usage.md) and the [parameter documentation](https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/parameters.md).
 
 ## Pipeline output
 
-For more details about the output files and reports, please refer to the
-[output documentation](https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/output.md).
+For more details about the output files and reports, please refer to the [output documentation](https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/output.md).
 
 ## Credits
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/tomte/1.0dev" target="_blank">nf-core/tomte</a>
+  This report has been generated by the <a href="https://github.com/nf-core/tomte/releases/tag/dev" target="_blank">nf-core/tomte</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/tomte/1.0dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/tomte/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-tomte-methods-description":
     order: -1000

conf/modules.config

@@ -38,6 +38,15 @@ process {
         ]
     }
 
+    withName: 'MULTIQC' {
+        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
 }
 
 //

docs/output.md

@@ -37,7 +37,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
 
-> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::note
+The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::
 
 ### MultiQC
 
@@ -64,6 +66,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
   - 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>
 

docs/usage.md

@@ -87,7 +87,9 @@ 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:
 
@@ -124,19 +126,25 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducbility, 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).
 

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
     //

modules.json

@@ -43,7 +43,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a33464f205fa15305bfe268546f6607b6f4d4753",
                         "installed_by": ["modules"]
                     },
                     "gatk4/asereadcounter": {

nextflow.config

@@ -76,9 +76,10 @@ params {
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes'
+    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
     validationShowHiddenParams       = false
     validate_params                  = true
+
 }
 
 // Load base.config by default for all pipelines
@@ -175,6 +176,7 @@ profiles {
     }
     apptainer {
         apptainer.enabled      = true
+        apptainer.autoMounts   = true
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -184,8 +186,8 @@ 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_full { includeConfig 'conf/test_full.config' }

nextflow_schema.json

@@ -88,14 +88,6 @@
                     "fa_icon": "fas fa-code-branch",
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified."
                 },
-                "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.",

workflows/tomte.nf

@@ -15,7 +15,7 @@ log.info logo + paramsSummaryLog(workflow) + citation
 
 WorkflowTomte.initialise(params, log)
 
-// TODO nf-core: Add all file path parameters for the pipeline to the list below
+// TODO nf-core: change this to use the plugin nf-validation
 // Check input path parameters to see if they exist
 def checkPathParamList = [
     params.input,
@@ -146,6 +146,16 @@ workflow TOMTE {
                                                               : Channel.empty()
     ch_vep_cache             = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") )  ? ch_references.vep_resources
                                                                 : ( params.vep_cache  ? Channel.fromPath(params.vep_cache).collect() : Channel.value([]) )
+    //
+    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    //
+    // INPUT_CHECK (
+    //    file(params.input)
+    // )
+    // ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
+    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
+    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
+    // ! There is currently no tooling to help you write a sample sheet schema
 
     //
     // MODULE: Run FastQC
@@ -281,6 +291,7 @@ workflow.onComplete {
     if (params.email || params.email_on_fail) {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
     }
+    NfcoreTemplate.dump_parameters(workflow, params)
     NfcoreTemplate.summary(workflow, params, log)
     if (params.hook_url) {
         NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)