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Important! Template update for nf-core/tools v2.11.1 #342

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3 changes: 3 additions & 0 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

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1 change: 1 addition & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/atac
- [ ] If necessary, also make a PR on the nf-core/atacseq _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>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
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4 changes: 2 additions & 2 deletions .github/workflows/fix-linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
token: ${{ secrets.nf_core_bot_auth_token }}

Expand All @@ -24,7 +24,7 @@ jobs:
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
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12 changes: 6 additions & 6 deletions .github/workflows/linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
Expand All @@ -27,9 +27,9 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install Prettier
run: npm install -g prettier
Expand All @@ -40,7 +40,7 @@ jobs:
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- name: Check code lints with Black
uses: psf/black@stable
Expand Down Expand Up @@ -71,7 +71,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
Expand Down
4 changes: 3 additions & 1 deletion .gitpod.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@ tasks:
command: |
pre-commit install --install-hooks
nextflow self-update

- name: unset JAVA_TOOL_OPTIONS
command: |
unset JAVA_TOOL_OPTIONS
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
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17 changes: 6 additions & 11 deletions README.md
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Expand Up @@ -30,11 +30,8 @@

## 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.

<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
Explain what rows and columns represent. For instance (please edit as appropriate):
Expand Down Expand Up @@ -63,11 +60,9 @@ nextflow run nf-core/atacseq \
--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/atacseq/usage) and the [parameter documentation](https://nf-co.re/atacseq/parameters).

Expand All @@ -94,7 +89,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
## Citations

<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use nf-core/atacseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
<!-- If you use nf-core/atacseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->

<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->

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2 changes: 1 addition & 1 deletion assets/multiqc_config.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/atacseq/releases/tag/dev" target="_blank">nf-core/atacseq</a>
This report has been generated by the <a href="https://github.com/nf-core/atacseq/tree/dev" target="_blank">nf-core/atacseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/atacseq/dev/docs/output" target="_blank">documentation</a>.
report_section_order:
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2 changes: 1 addition & 1 deletion assets/slackreport.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
{
"fallback": "Plain-text summary of the attachment.",
"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
"author_name": "nf-core/atacseq v${version} - ${runName}",
"author_name": "nf-core/atacseq ${version} - ${runName}",
"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
"fields": [
Expand Down
2 changes: 1 addition & 1 deletion conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ process {
}

withName: 'MULTIQC' {
ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: params.publish_dir_mode,
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4 changes: 2 additions & 2 deletions docs/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ You will need to create a samplesheet with information about the samples you wou

The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:

```console
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
Expand All @@ -33,7 +33,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th

A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.

```console
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
Expand Down
32 changes: 18 additions & 14 deletions lib/NfcoreTemplate.groovy
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@

import org.yaml.snakeyaml.Yaml
import groovy.json.JsonOutput
import nextflow.extension.FilesEx

class NfcoreTemplate {

Expand Down Expand Up @@ -141,12 +142,14 @@ class NfcoreTemplate {
try {
if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
sendmail_tf.withWriter { w -> w << sendmail_html }
[ 'sendmail', '-t' ].execute() << sendmail_html
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
} catch (all) {
// Catch failures and try with plaintext
def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
mail_cmd += [ '-A', mqc_report ]
}
mail_cmd.execute() << email_html
Expand All @@ -155,14 +158,16 @@ class NfcoreTemplate {
}

// Write summary e-mail HTML to a file
def output_d = new File("${params.outdir}/pipeline_info/")
if (!output_d.exists()) {
output_d.mkdirs()
}
def output_hf = new File(output_d, "pipeline_report.html")
def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
output_hf.withWriter { w -> w << email_html }
def output_tf = new File(output_d, "pipeline_report.txt")
FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html");
output_hf.delete()

// Write summary e-mail TXT to a file
def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
output_tf.withWriter { w -> w << email_txt }
FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
output_tf.delete()
}

//
Expand Down Expand Up @@ -227,15 +232,14 @@ 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_${timestamp}.json")
def filename = "params_${timestamp}.json"
def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
def jsonStr = JsonOutput.toJson(params)
output_pf.text = JsonOutput.prettyPrint(jsonStr)
temp_pf.text = JsonOutput.prettyPrint(jsonStr)

FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
temp_pf.delete()
}

//
Expand Down
6 changes: 3 additions & 3 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -7,17 +7,17 @@
"nf-core": {
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "4ab13872435962dadc239979554d13709e20bf29",
"installed_by": ["modules"]
}
}
Expand Down
7 changes: 7 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/environment.yml

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6 changes: 3 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf

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7 changes: 4 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/meta.yml

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38 changes: 38 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test

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2 changes: 2 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/fastqc/environment.yml

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