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Nf core template update #461

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Dec 21, 2023
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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 @@ -20,6 +20,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rare
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test_one_sample,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 @@ -31,7 +31,7 @@ jobs:
- "-profile test_one_sample,docker"
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: 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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15 changes: 5 additions & 10 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -101,11 +101,8 @@ Note that it is possible to include/exclude certain tools or steps.

## 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 @@ -129,11 +126,9 @@ nextflow run nf-core/raredisease \
--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/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).

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2 changes: 1 addition & 1 deletion assets/multiqc_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ custom_logo_url: https://github.com/nf-core/raredisease/
custom_logo_title: "nf-core/raredisease"

report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/dev" target="_blank">nf-core/raredisease</a>
This report has been generated by the <a href="https://github.com/nf-core/raredisease/tree/dev" target="_blank">nf-core/raredisease</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/raredisease/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/raredisease v${version} - ${runName}",
"author_name": "nf-core/raredisease ${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/raredisease.config
Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,7 @@ process {

process {
withName: '.*RAREDISEASE: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,
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
8 changes: 4 additions & 4 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@
},
"cat/cat": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2",
"installed_by": ["modules"]
},
"chromograph": {
Expand All @@ -92,7 +92,7 @@
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
"git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
"installed_by": ["modules"]
},
"deepvariant": {
Expand Down Expand Up @@ -122,7 +122,7 @@
},
"fastqc": {
"branch": "master",
"git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"installed_by": ["modules"]
},
"gatk4/bedtointervallist": {
Expand Down Expand Up @@ -279,7 +279,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
"git_sha": "4ab13872435962dadc239979554d13709e20bf29",
"installed_by": ["modules"]
},
"ngsbits/samplegender": {
Expand Down
7 changes: 7 additions & 0 deletions modules/nf-core/cat/cat/environment.yml

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14 changes: 11 additions & 3 deletions modules/nf-core/cat/cat/main.nf

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

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