diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000000000000000000000000000000000000..ea27a5843a0ff5f97ef49908689f595c42e17a1f
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,27 @@
+{
+ "name": "nfcore",
+ "image": "nfcore/gitpod:latest",
+ "remoteUser": "gitpod",
+
+ // Configure tool-specific properties.
+ "customizations": {
+ // Configure properties specific to VS Code.
+ "vscode": {
+ // Set *default* container specific settings.json values on container create.
+ "settings": {
+ "python.defaultInterpreterPath": "/opt/conda/bin/python",
+ "python.linting.enabled": true,
+ "python.linting.pylintEnabled": true,
+ "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+ "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+ "python.linting.flake8Path": "/opt/conda/bin/flake8",
+ "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+ "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+ "python.linting.pylintPath": "/opt/conda/bin/pylint"
+ },
+
+ // Add the IDs of extensions you want installed when the container is created.
+ "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+ }
+ }
+}
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/workflows/ci.yml b/.github/workflows/ci.yml
index f2fd3486eef41716a3630c93abc3f3bca0f0abc2..cafa44a9680031ad06866987ee8e5e74a23babdd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,6 +11,10 @@ on:
env:
NXF_ANSI_LOG: false
+concurrency:
+ group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+ cancel-in-progress: true
+
jobs:
test:
name: Run pipeline with test data
@@ -20,11 +24,11 @@ jobs:
strategy:
matrix:
NXF_VER:
- - "21.10.3"
+ - "22.10.1"
- "latest-everything"
steps:
- name: Check out pipeline code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 502eff95019714bf6b719046f0127d1e998f6b8a..3d885115b60b0bf1064b69dcf067211d0ce95f38 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -24,7 +24,7 @@ jobs:
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
- - uses: actions/setup-node@v2
+ - uses: actions/setup-node@v3
- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
id: prettier_status
run: |
if prettier --check ${GITHUB_WORKSPACE}; then
- echo "::set-output name=result::pass"
+ echo "name=result::pass" >> $GITHUB_OUTPUT
else
- echo "::set-output name=result::fail"
+ echo "name=result::fail" >> $GITHUB_OUTPUT
fi
- name: Run 'prettier --write'
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8a5ce69b89514cf50a7efb930005ebc4f47074df..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
@@ -38,7 +40,7 @@ jobs:
PythonBlack:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
- name: Check code lints with Black
uses: psf/black@stable
@@ -69,12 +71,12 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
- - uses: actions/setup-python@v3
+ - uses: actions/setup-python@v4
with:
python-version: "3.7"
architecture: "x64"
@@ -97,7 +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 eb74a5741c8dd660549f4b79b6a37619eec57dc3..437d763d0c2c8fdeb5f8f7e1e04d54771d9b46d6 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,5 +1,6 @@
email_template.html
adaptivecard.json
+slackreport.json
.nextflow*
work/
data/
@@ -8,3 +9,4 @@ results/
testing/
testing*
*.pyc
+bin/
diff --git a/CITATION.cff b/CITATION.cff
deleted file mode 100644
index 017666c018477b09570b3b82c33abdbaa471cbbc..0000000000000000000000000000000000000000
--- a/CITATION.cff
+++ /dev/null
@@ -1,56 +0,0 @@
-cff-version: 1.2.0
-message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
-authors:
- - family-names: Ewels
- given-names: Philip
- - family-names: Peltzer
- given-names: Alexander
- - family-names: Fillinger
- given-names: Sven
- - family-names: Patel
- given-names: Harshil
- - family-names: Alneberg
- given-names: Johannes
- - family-names: Wilm
- given-names: Andreas
- - family-names: Garcia
- given-names: Maxime Ulysse
- - family-names: Di Tommaso
- given-names: Paolo
- - family-names: Nahnsen
- given-names: Sven
-title: "The nf-core framework for community-curated bioinformatics pipelines."
-version: 2.4.1
-doi: 10.1038/s41587-020-0439-x
-date-released: 2022-05-16
-url: https://github.com/nf-core/tools
-prefered-citation:
- type: article
- authors:
- - family-names: Ewels
- given-names: Philip
- - family-names: Peltzer
- given-names: Alexander
- - family-names: Fillinger
- given-names: Sven
- - family-names: Patel
- given-names: Harshil
- - family-names: Alneberg
- given-names: Johannes
- - family-names: Wilm
- given-names: Andreas
- - family-names: Garcia
- given-names: Maxime Ulysse
- - family-names: Di Tommaso
- given-names: Paolo
- - family-names: Nahnsen
- given-names: Sven
- doi: 10.1038/s41587-020-0439-x
- journal: nature biotechnology
- start: 276
- end: 278
- title: "The nf-core framework for community-curated bioinformatics pipelines."
- issue: 3
- volume: 38
- year: 2020
- url: https://dx.doi.org/10.1038/s41587-020-0439-x
diff --git a/README.md b/README.md
index 700fddecaeaa63eedb29d065ced045a5ed4e913e..b2c63a1ffc96f8aa3329efcbdca6f2c2cef1e69d 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
[](https://nf-co.re/hic/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
-[](https://www.nextflow.io/)
+[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
@@ -31,7 +31,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
## Quick Start
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
diff --git a/assets/slackreport.json b/assets/slackreport.json
new file mode 100644
index 0000000000000000000000000000000000000000..043d02f27570da8e53dd7d3dd6d0a640cfa4636d
--- /dev/null
+++ b/assets/slackreport.json
@@ -0,0 +1,34 @@
+{
+ "attachments": [
+ {
+ "fallback": "Plain-text summary of the attachment.",
+ "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+ "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+ "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+ "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+ "fields": [
+ {
+ "title": "Command used to launch the workflow",
+ "value": "```${commandLine}```",
+ "short": false
+ }
+ <%
+ if (!success) { %>
+ ,
+ {
+ "title": "Full error message",
+ "value": "```${errorReport}```",
+ "short": false
+ },
+ {
+ "title": "Pipeline configuration",
+ "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+ "short": false
+ }
+ <% }
+ %>
+ ],
+ "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+ }
+ ]
+}
diff --git a/docs/usage.md b/docs/usage.md
index 59554a13ba962d13893b3c3739a1a0289a0215c9..e0dab28a5e3b6e3b06d599b7009ce054c99fb76f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -83,9 +83,9 @@ nextflow pull nf-core/hic
It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
-First, go to the [nf-core/hic releases page](https://github.com/nf-core/hic/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
+First, go to the [nf-core/hic releases page](https://github.com/nf-core/hic/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
## Core Nextflow arguments
@@ -95,7 +95,7 @@ This version number will be logged in reports when you run the pipeline, so that
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, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/).
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, 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.
@@ -104,8 +104,11 @@ The pipeline also dynamically loads configurations from [https://github.com/nf-c
Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
They are loaded in sequence, so later profiles can overwrite earlier profiles.
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
+- `test`
+ - A profile with a complete configuration for automated testing
+ - Includes links to test data so needs no other parameters
- `docker`
- A generic configuration profile to be used with [Docker](https://docker.com/)
- `singularity`
@@ -118,9 +121,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
- `conda`
- A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
-- `test`
- - A profile with a complete configuration for automated testing
- - Includes links to test data so needs no other parameters
### `-resume`
@@ -169,8 +169,14 @@ Work dir:
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
```
+#### For beginners
+
+A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below.
+
+#### Advanced option on process level
+
To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN).
-We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`.
+We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`.
If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9).
The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements.
The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB.
@@ -189,7 +195,7 @@ process {
>
> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
-### Updating containers
+### Updating containers (advanced users)
The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
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 27feb009a1c51523871e0b6c9a52662fe38fe322..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
@@ -146,10 +165,10 @@ class NfcoreTemplate {
}
//
- // Construct and send adaptive card
- // https://adaptivecards.io
+ // Construct and send a notification to a web server as JSON
+ // e.g. Microsoft Teams and Slack
//
- public static void adaptivecard(workflow, params, summary_params, projectDir, log) {
+ public static void IM_notification(workflow, params, summary_params, projectDir, log) {
def hook_url = params.hook_url
def summary = [:]
@@ -170,7 +189,7 @@ class NfcoreTemplate {
misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp
def msg_fields = [:]
- msg_fields['version'] = workflow.manifest.version
+ msg_fields['version'] = NfcoreTemplate.version(workflow)
msg_fields['runName'] = workflow.runName
msg_fields['success'] = workflow.success
msg_fields['dateComplete'] = workflow.complete
@@ -178,13 +197,16 @@ class NfcoreTemplate {
msg_fields['exitStatus'] = workflow.exitStatus
msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
msg_fields['errorReport'] = (workflow.errorReport ?: 'None')
- msg_fields['commandLine'] = workflow.commandLine
+ 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()
- def hf = new File("$projectDir/assets/adaptivecard.json")
+ // Different JSON depending on the service provider
+ // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+ def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+ def hf = new File("$projectDir/assets/${json_path}")
def json_template = engine.createTemplate(hf).make(msg_fields)
def json_message = json_template.toString()
@@ -209,7 +231,7 @@ class NfcoreTemplate {
if (workflow.stats.ignoredCount == 0) {
log.info "-${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}-"
@@ -297,6 +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)}
@@ -305,7 +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()
)
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 30096e75ba42f425596ac3ca572eaf73c2d66d87..461d1bc42f3e2df82762eabcfab7c57e76e6791a 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -19,7 +19,7 @@ class WorkflowMain {
}
//
- // Print help to screen if required
+ // Generate help string
//
public static String help(workflow, params, log) {
def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
@@ -32,7 +32,7 @@ class WorkflowMain {
}
//
- // Print parameter summary log to screen
+ // Generate parameter summary log string
//
public static String paramsSummaryLog(workflow, params, log) {
def summary_log = ''
@@ -53,15 +53,21 @@ class WorkflowMain {
System.exit(0)
}
- // Validate workflow parameters via the JSON schema
- if (params.validate_params) {
- NfcoreSchema.validateParameters(workflow, params, log)
+ // Print workflow version and exit on --version
+ if (params.version) {
+ String workflow_version = NfcoreTemplate.version(workflow)
+ log.info "${workflow.manifest.name} ${workflow_version}"
+ System.exit(0)
}
// Print parameter summary log to screen
-
log.info paramsSummaryLog(workflow, params, log)
+ // Validate workflow parameters via the JSON schema
+ if (params.validate_params) {
+ NfcoreSchema.validateParameters(workflow, params, log)
+ }
+
// Check that a -profile or Nextflow config has been provided to run the pipeline
NfcoreTemplate.checkConfigProvided(workflow, log)
diff --git a/modules.json b/modules.json
index bf0b530298643db9c7c982acdbba3d944c71d3c6..9bcc9edcadb7f67ada8233c1d2c87e878ccf6be2 100644
--- a/modules.json
+++ b/modules.json
@@ -7,15 +7,18 @@
"nf-core": {
"custom/dumpsoftwareversions": {
"branch": "master",
- "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+ "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+ "installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
- "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+ "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+ "installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
- "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+ "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+ "installed_by": ["modules"]
}
}
}
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 31f62fa99c98fdf3938dd5a360c5d4e522479704..f418a8f51475451470c872f4b4e6ee51f55bfa86 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -1,5 +1,6 @@
process SAMPLESHEET_CHECK {
tag "$samplesheet"
+ label 'process_single'
conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -13,6 +14,9 @@ process SAMPLESHEET_CHECK {
path '*.csv' , emit: csv
path "versions.yml", emit: versions
+ when:
+ task.ext.when == null || task.ext.when
+
script: // This script is bundled with the pipeline, in nf-core/hic/bin/
"""
check_samplesheet.py \\
diff --git a/nextflow.config b/nextflow.config
index aa17ff888d68a8a62e40a8c11bc55c731dded0b4..9138dbeacdab9df5fcd9f4215916e9c38e4b4d0b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -35,6 +35,7 @@ params {
monochrome_logs = false
hook_url = null
help = false
+ version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
@@ -81,6 +82,7 @@ profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
+ conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
@@ -89,6 +91,7 @@ profiles {
}
mamba {
params.enable_conda = true
+ conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
@@ -104,6 +107,9 @@ profiles {
shifter.enabled = false
charliecloud.enabled = false
}
+ arm {
+ docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+ }
singularity {
singularity.enabled = true
singularity.autoMounts = true
@@ -185,11 +191,11 @@ dag {
manifest {
name = 'nf-core/hic'
- author = 'Nicolas Servant'
+ author = """Nicolas Servant"""
homePage = 'https://github.com/nf-core/hic'
- description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
+ description = """Analysis of Chromosome Conformation Capture data (Hi-C)"""
mainScript = 'main.nf'
- nextflowVersion = '!>=21.10.3'
+ nextflowVersion = '!>=22.10.1'
version = '1.4.0dev'
doi = ''
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3d71df880abbf48ad8e9d0ffeb39b0487986d9d1..93eaa7de1f9b5c8a85d7428cbe45ccdc4f55466b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -176,6 +176,12 @@
"fa_icon": "fas fa-question-circle",
"hidden": true
},
+ "version": {
+ "type": "boolean",
+ "description": "Display version and exit.",
+ "fa_icon": "fas fa-question-circle",
+ "hidden": true
+ },
"publish_dir_mode": {
"type": "string",
"default": "copy",
@@ -217,7 +223,7 @@
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
- "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.",
+ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
diff --git a/workflows/hic.nf b/workflows/hic.nf
index abc5411a5d3bf49e34775c68b679fc62641c7690..ee80787d91dbc8838924bc2525eabe5d10981c50 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -82,7 +82,7 @@ workflow HIC {
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
CUSTOM_DUMPSOFTWAREVERSIONS (
- ch_versions.unique().collectFile(name: 'collated_versions.yml')
+ ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
)
//
@@ -102,12 +102,11 @@ workflow HIC {
MULTIQC (
ch_multiqc_files.collect(),
- ch_multiqc_config.collect().ifEmpty([]),
- ch_multiqc_custom_config.collect().ifEmpty([]),
- ch_multiqc_logo.collect().ifEmpty([])
+ ch_multiqc_config.toList(),
+ ch_multiqc_custom_config.toList(),
+ ch_multiqc_logo.toList()
)
multiqc_report = MULTIQC.out.report.toList()
- ch_versions = ch_versions.mix(MULTIQC.out.versions)
}
/*
@@ -122,7 +121,7 @@ workflow.onComplete {
}
NfcoreTemplate.summary(workflow, params, log)
if (params.hook_url) {
- NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log)
+ NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
}
}