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Merge pull request #1025 from nf-core/nf-core-template-merge-2.10
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Important! Template update for nf-core/tools v2.10
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scarlhoff authored Oct 6, 2023
2 parents 6d44207 + 4bf3681 commit bc9c7b5
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1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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Expand Up @@ -2,6 +2,7 @@
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
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4 changes: 3 additions & 1 deletion .github/CONTRIBUTING.md
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Expand Up @@ -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/eager then the best place to ask is on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/eager then the best place to ask is on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::

## Contribution workflow

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2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
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Expand Up @@ -78,7 +78,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "3.8"
python-version: "3.11"
architecture: "x64"

- name: Install dependencies
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68 changes: 68 additions & 0 deletions .github/workflows/release-announcments.yml
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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/[email protected]
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 }}
#
2 changes: 1 addition & 1 deletion CITATIONS.md
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Expand Up @@ -12,7 +12,7 @@

- [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].
- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

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133 changes: 102 additions & 31 deletions CODE_OF_CONDUCT.md

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21 changes: 12 additions & 9 deletions README.md
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Expand Up @@ -2,7 +2,8 @@

**A fully reproducible and state-of-the-art ancient DNA analysis pipeline.**

[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/eager/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/nf-core/eager/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/eager/actions?query=workflow%3A%22nf-core+CI%22)
[![GitHub Actions Linting Status](https://github.com/nf-core/eager/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/eager/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/eager/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1465061-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1465061)

[![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/)
Expand Down Expand Up @@ -84,10 +85,11 @@ A graphical overview of suggested routes through the pipeline depending on conte

## 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:

Expand All @@ -112,10 +114,11 @@ nextflow run nf-core/eager \
--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 and further functionality, please refer to the [usage documentation](https://nf-co.re/eager/usage) and the [parameter documentation](https://nf-co.re/eager/parameters).

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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/eager/3.0.0dev" target="_blank">nf-core/eager</a>
This report has been generated by the <a href="https://github.com/nf-core/eager/releases/tag/dev" target="_blank">nf-core/eager</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/eager/3.0.0dev/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/eager/dev/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-eager-methods-description":
order: -1000
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9 changes: 9 additions & 0 deletions conf/modules.config
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Expand Up @@ -55,6 +55,15 @@ 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 }
]
}

withName: FALCO {
tag = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
ext.args = '--quiet'
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5 changes: 5 additions & 0 deletions docs/output.md
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Expand Up @@ -39,6 +39,10 @@ FastQC results in the `raw/` directory contain the results of running FastQC on

![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)

:::note
The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
:::

### MultiQC

<details markdown="1">
Expand All @@ -64,6 +68,7 @@ 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>

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16 changes: 12 additions & 4 deletions docs/usage.md
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Expand Up @@ -117,7 +117,9 @@ 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:

Expand Down Expand Up @@ -154,19 +156,25 @@ 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).

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16 changes: 16 additions & 0 deletions lib/NfcoreTemplate.groovy
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Expand Up @@ -3,6 +3,7 @@
//

import org.yaml.snakeyaml.Yaml
import groovy.json.JsonOutput

class NfcoreTemplate {

Expand Down Expand Up @@ -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
//
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2 changes: 1 addition & 1 deletion lib/WorkflowEager.groovy
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Expand Up @@ -52,7 +52,7 @@ class WorkflowEager {

public static String toolCitationText(params) {

// TODO Optionally add in-text citation tools to this list.
// TODO nf-core: Optionally add in-text citation tools to this list.
// 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 citation_text = [
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3 changes: 3 additions & 0 deletions main.nf
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Expand Up @@ -17,6 +17,9 @@ nextflow.enable.dsl = 2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// TODO nf-core: Remove this line if you don't need a FASTA file
// This is an example of how to use getGenomeAttribute() to fetch parameters
// from igenomes.config using `--genome`
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')

/*
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4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -22,7 +22,7 @@
},
"bamutil/trimbam": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bbmap/bbduk": {
Expand Down Expand Up @@ -107,7 +107,7 @@
},
"fastqc": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
"installed_by": ["modules"]
},
"gunzip": {
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2 changes: 1 addition & 1 deletion modules/nf-core/bamutil/trimbam/main.nf

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6 changes: 5 additions & 1 deletion modules/nf-core/fastqc/main.nf

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7 changes: 4 additions & 3 deletions nextflow.config
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Expand Up @@ -64,7 +64,7 @@ params {
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes'
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true

Expand Down Expand Up @@ -297,6 +297,7 @@ profiles {
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
Expand All @@ -306,8 +307,8 @@ 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' }
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