diff --git a/.gitattributes b/.gitattributes
index 050bb1203530c3ee0b610fe2a05aed5059a3bf19..7a2dabc29354bc42709be9241603cff642ce5c27 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,4 @@
*.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 21343c4d8ef64758fbfe436553442d6a857c7024..3b558e400aaa1d5349ba9a3ca945664302ca189f 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
### Images and figures
For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/hic/codespaces)
+- Tools installed
+ - nf-core
+ - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 98a7950ce9bef303424ad5ce1c10c1c6ed135f1d..e405327c328cc2a94ebadf33e9ac4cad766f7461 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,7 +42,7 @@ body:
attributes:
label: System information
description: |
- * Nextflow version _(eg. 21.10.3)_
+ * Nextflow version _(eg. 22.10.1)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 56233aa3631298e9a762b06c6f868ee171b41773..c67458d182e840707cbccc6914ff1e3d95331b0e 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/
- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
- - [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/hic _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>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 77358dee77fafceacab736de94ae79f2258a523f..858d622efc884fba438eb48c80d4122443dfa3a0 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -4,6 +4,8 @@ name: nf-core linting
# that the code meets the nf-core guidelines.
on:
push:
+ branches:
+ - dev
pull_request:
release:
types: [published]
@@ -12,9 +14,9 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
- - uses: actions/setup-node@v2
+ - uses: actions/setup-node@v3
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
@@ -25,9 +27,9 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
- - uses: actions/setup-node@v2
+ - uses: actions/setup-node@v3
- name: Install Prettier
run: npm install -g prettier
@@ -35,22 +37,48 @@ jobs:
- name: Run Prettier --check
run: prettier --check ${GITHUB_WORKSPACE}
+ PythonBlack:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v3
+
+ - name: Check code lints with Black
+ uses: psf/black@stable
+
+ # If the above check failed, post a comment on the PR explaining the failure
+ - name: Post PR comment
+ if: failure()
+ uses: mshick/add-pr-comment@v1
+ with:
+ message: |
+ ## Python linting (`black`) is failing
+
+ To keep the code consistent with lots of contributors, we run automated code consistency checks.
+ To fix this CI test, please run:
+
+ * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+ * Fix formatting errors in your pipeline: `black .`
+
+ Once you push these changes the test should pass, and you can hide this comment :+1:
+
+ We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+ Thanks again for your contribution!
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+ allow-repeats: false
+
nf-core:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
- name: Install Nextflow
- env:
- CAPSULE_LOG: none
- run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
+ uses: nf-core/setup-nextflow@v1
- - uses: actions/setup-python@v3
+ - uses: actions/setup-python@v4
with:
- python-version: "3.6"
+ python-version: "3.7"
architecture: "x64"
- name: Install dependencies
@@ -71,7 +99,7 @@ jobs:
- name: Upload linting log file artifact
if: ${{ always() }}
- uses: actions/upload-artifact@v2
+ uses: actions/upload-artifact@v3
with:
name: linting-logs
path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 04758f61e368b37a7651aff015e51a9c31162542..3963518629ae2716fe449b47975a3a22187a1513 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
- name: Get PR number
id: pr_number
- run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+ run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
- name: Post PR comment
uses: marocchino/sticky-pull-request-comment@v2
diff --git a/.prettierignore b/.prettierignore
index d0e7ae58916d32ec5fc706ae0eda9403db44f290..437d763d0c2c8fdeb5f8f7e1e04d54771d9b46d6 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,4 +1,6 @@
email_template.html
+adaptivecard.json
+slackreport.json
.nextflow*
work/
data/
@@ -7,3 +9,4 @@ results/
testing/
testing*
*.pyc
+bin/
diff --git a/assets/email_template.txt b/assets/email_template.txt
index a951c5e7f965fa5829707fc84f4351495995190f..6905d6fc70619b99a53a9c51670b026095e2965f 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -6,7 +6,6 @@
`._,._,'
nf-core/hic v${version}
----------------------------------------------------
-
Run Name: $runName
<% if (success){
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index b3d092f8090902661a13b951bb251af4645f8d80..33cd4f6e8df62276afa55ab4c00cd59900ea013e 100755
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -46,7 +46,6 @@ class NfcoreSchema {
'quiet',
'syslog',
'v',
- 'version',
// Options for `nextflow run` command
'ansi',
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 2fc0a9b9b61d85455653e2abbc91391f8b8606b0..25a0a74a645332b1cacfc99b6e5c9c4500c49423 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -32,6 +32,25 @@ class NfcoreTemplate {
}
}
+ //
+ // Generate version string
+ //
+ public static String version(workflow) {
+ String version_string = ""
+
+ if (workflow.manifest.version) {
+ def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+ version_string += "${prefix_v}${workflow.manifest.version}"
+ }
+
+ if (workflow.commitId) {
+ def git_shortsha = workflow.commitId.substring(0, 7)
+ version_string += "-g${git_shortsha}"
+ }
+
+ return version_string
+ }
+
//
// Construct and send completion email
//
@@ -61,7 +80,7 @@ class NfcoreTemplate {
misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
def email_fields = [:]
- email_fields['version'] = workflow.manifest.version
+ email_fields['version'] = NfcoreTemplate.version(workflow)
email_fields['runName'] = workflow.runName
email_fields['success'] = workflow.success
email_fields['dateComplete'] = workflow.complete
@@ -145,6 +164,64 @@ class NfcoreTemplate {
output_tf.withWriter { w -> w << email_txt }
}
+ //
+ // Construct and send a notification to a web server as JSON
+ // e.g. Microsoft Teams and Slack
+ //
+ public static void IM_notification(workflow, params, summary_params, projectDir, log) {
+ def hook_url = params.hook_url
+
+ def summary = [:]
+ for (group in summary_params.keySet()) {
+ summary << summary_params[group]
+ }
+
+ def misc_fields = [:]
+ misc_fields['start'] = workflow.start
+ misc_fields['complete'] = workflow.complete
+ misc_fields['scriptfile'] = workflow.scriptFile
+ misc_fields['scriptid'] = workflow.scriptId
+ if (workflow.repository) misc_fields['repository'] = workflow.repository
+ if (workflow.commitId) misc_fields['commitid'] = workflow.commitId
+ if (workflow.revision) misc_fields['revision'] = workflow.revision
+ misc_fields['nxf_version'] = workflow.nextflow.version
+ misc_fields['nxf_build'] = workflow.nextflow.build
+ misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp
+
+ def msg_fields = [:]
+ msg_fields['version'] = NfcoreTemplate.version(workflow)
+ msg_fields['runName'] = workflow.runName
+ msg_fields['success'] = workflow.success
+ msg_fields['dateComplete'] = workflow.complete
+ msg_fields['duration'] = workflow.duration
+ msg_fields['exitStatus'] = workflow.exitStatus
+ msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+ msg_fields['errorReport'] = (workflow.errorReport ?: 'None')
+ msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+ msg_fields['projectDir'] = workflow.projectDir
+ msg_fields['summary'] = summary << misc_fields
+
+ // Render the JSON template
+ def engine = new groovy.text.GStringTemplateEngine()
+ // Different JSON depending on the service provider
+ // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+ def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+ def hf = new File("$projectDir/assets/${json_path}")
+ def json_template = engine.createTemplate(hf).make(msg_fields)
+ def json_message = json_template.toString()
+
+ // POST
+ def post = new URL(hook_url).openConnection();
+ post.setRequestMethod("POST")
+ post.setDoOutput(true)
+ post.setRequestProperty("Content-Type", "application/json")
+ post.getOutputStream().write(json_message.getBytes("UTF-8"));
+ def postRC = post.getResponseCode();
+ if (! postRC.equals(200)) {
+ log.warn(post.getErrorStream().getText());
+ }
+ }
+
//
// Print pipeline summary on completion
//
@@ -154,7 +231,7 @@ class NfcoreTemplate {
if (workflow.stats.ignoredCount == 0) {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
} else {
- log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+ log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
}
} else {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
@@ -242,6 +319,7 @@ class NfcoreTemplate {
//
public static String logo(workflow, monochrome_logs) {
Map colors = logColours(monochrome_logs)
+ String workflow_version = NfcoreTemplate.version(workflow)
String.format(
"""\n
${dashedLine(monochrome_logs)}
@@ -250,7 +328,7 @@ class NfcoreTemplate {
${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset}
${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset}
${colors.green}`._,._,\'${colors.reset}
- ${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+ ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset}
${dashedLine(monochrome_logs)}
""".stripIndent()
)