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/.editorconfig b/.editorconfig
index 43c7138733277a83ffc7e788e0283df17f6ccf71..75c2fe61f4886762396871469bba8684f282add2 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
indent_size = 2
# These files are edited and tested upstream in nf-core/modules
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 82c1a4ecd1bac8b5410b2825e230f9f3924594d3..c528fffcb40acc23443d90b0eb8f0922cfb265f2 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -28,3 +28,7 @@ jobs:
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
+ - uses: actions/upload-artifact@v3
+ with:
+ name: Tower debug log file
+ path: tower_action_*.log
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 5cd0714273dca87007b7c5ea50df27d05fe3606d..3f9b365ffe5729722f94316715fe5e654860c152 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -23,3 +23,7 @@ jobs:
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
+ - uses: actions/upload-artifact@v3
+ with:
+ name: Tower debug log file
+ path: tower_action_*.log
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0dac5c2786f66f7e503085c858823a4833afb92a..5531e307166fc8f4d5717ba3efc646693560c67b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,7 +10,10 @@ on:
env:
NXF_ANSI_LOG: false
- CAPSULE_LOG: none
+
+concurrency:
+ group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+ cancel-in-progress: true
jobs:
test:
@@ -20,27 +23,17 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
- # Nextflow versions
- include:
- # Test pipeline minimum Nextflow version
- - NXF_VER: "21.10.3"
- NXF_EDGE: ""
- # Test latest edge release of Nextflow
- - NXF_VER: ""
- NXF_EDGE: "1"
+ NXF_VER:
+ - "22.10.1"
+ - "latest-everything"
steps:
- name: Check out pipeline code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
- name: Install Nextflow
- env:
- NXF_VER: ${{ matrix.NXF_VER }}
- # Uncomment only if the edge release is more recent than the latest stable release
- # See https://github.com/nextflow-io/nextflow/issues/2467
- # NXF_EDGE: ${{ matrix.NXF_EDGE }}
- run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
+ uses: nf-core/setup-nextflow@v1
+ with:
+ version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with test data
run: |
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 502eff95019714bf6b719046f0127d1e998f6b8a..66550055794ba4b8fa3458edcf8a3e33de57dc30 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 "result=pass" >> $GITHUB_OUTPUT
else
- echo "::set-output name=result::fail"
+ echo "result=fail" >> $GITHUB_OUTPUT
fi
- name: Run 'prettier --write'
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 3963518629ae2716fe449b47975a3a22187a1513..0bbcd30f23effefe9ac5a7a49cc16f43140c20a7 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
- name: Get PR number
id: pr_number
- run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+ run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
- name: Post PR comment
uses: marocchino/sticky-pull-request-comment@v2
diff --git a/README.md b/README.md
index 48a23b070e337e18fd7ceb230d4aa802f7bdd4e5..0a5b6a852880113f09a00707ed136818f44e6292 100644
--- a/README.md
+++ b/README.md
@@ -1,19 +1,14 @@
#  
-[](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+CI%22)
-[](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+linting%22)
-[](https://nf-co.re/hic/results)
-[](https://doi.org/10.5281/zenodo.XXXXXXX)
-
-[](https://www.nextflow.io/)
-[](https://docs.conda.io/en/latest/)
-[](https://www.docker.com/)
-[](https://sylabs.io/docs/)
+[](https://nf-co.re/hic/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
+
+[](https://www.nextflow.io/)
+[](https://docs.conda.io/en/latest/)
+[](https://www.docker.com/)
+[](https://sylabs.io/docs/)
[](https://tower.nf/launch?pipeline=https://github.com/nf-core/hic)
-[](https://nfcore.slack.com/channels/hic)
-[](https://twitter.com/nf_core)
-[](https://www.youtube.com/c/nf-core)
+[](https://nfcore.slack.com/channels/hic)[](https://twitter.com/nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
@@ -21,7 +16,7 @@
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. 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. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
-On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hic/results).
+On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hic/results).
## Pipeline summary
@@ -43,13 +38,13 @@ 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))_.
3. Download the pipeline and test it on a minimal dataset with a single command:
- ```console
+ ```bash
nextflow run nf-core/hic -profile test,YOURPROFILE --outdir <OUTDIR>
```
@@ -62,7 +57,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
4. Start running your own analysis!
- ```console
+ ```bash
nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
new file mode 100644
index 0000000000000000000000000000000000000000..79f9dbe9924bf336c47a8ad509ae5bf68e430640
--- /dev/null
+++ b/assets/adaptivecard.json
@@ -0,0 +1,67 @@
+{
+ "type": "message",
+ "attachments": [
+ {
+ "contentType": "application/vnd.microsoft.card.adaptive",
+ "contentUrl": null,
+ "content": {
+ "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+ "msteams": {
+ "width": "Full"
+ },
+ "type": "AdaptiveCard",
+ "version": "1.2",
+ "body": [
+ {
+ "type": "TextBlock",
+ "size": "Large",
+ "weight": "Bolder",
+ "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
+ "text": "nf-core/hic v${version} - ${runName}",
+ "wrap": true
+ },
+ {
+ "type": "TextBlock",
+ "spacing": "None",
+ "text": "Completed at ${dateComplete} (duration: ${duration})",
+ "isSubtle": true,
+ "wrap": true
+ },
+ {
+ "type": "TextBlock",
+ "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
+ "wrap": true
+ },
+ {
+ "type": "TextBlock",
+ "text": "The command used to launch the workflow was as follows:",
+ "wrap": true
+ },
+ {
+ "type": "TextBlock",
+ "text": "${commandLine}",
+ "isSubtle": true,
+ "wrap": true
+ }
+ ],
+ "actions": [
+ {
+ "type": "Action.ShowCard",
+ "title": "Pipeline Configuration",
+ "card": {
+ "type": "AdaptiveCard",
+ "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+ "body": [
+ {
+ "type": "FactSet",
+ "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
+ ]
+ }
+ ]
+ }
+ }
+ ]
+ }
+ }
+ ]
+}
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
new file mode 100644
index 0000000000000000000000000000000000000000..5b51ef5abc4fbe18bf0da19167f4d0506e14d0a2
--- /dev/null
+++ b/assets/methods_description_template.yml
@@ -0,0 +1,25 @@
+id: "nf-core-hic-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "nf-core/hic Methods Description"
+section_href: "https://github.com/nf-core/hic"
+plot_type: "html"
+## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## You inject any metadata in the Nextflow '${workflow}' object
+data: |
+ <h4>Methods</h4>
+ <p>Data was processed using nf-core/hic v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
+ <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
+ <pre><code>${workflow.commandLine}</code></pre>
+ <h4>References</h4>
+ <ul>
+ <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
+ <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+ </ul>
+ <div class="alert alert-info">
+ <h5>Notes:</h5>
+ <ul>
+ ${nodoi_text}
+ <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+ <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+ </ul>
+ </div>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index e371ccf83ba8d11c96891ddae6c55e120e370667..b2cf07d846fa86aa4100cd1ac05fd72b3827dde4 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -3,9 +3,11 @@ report_comment: >
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/hic" target="_blank">documentation</a>.
report_section_order:
- software_versions:
+ "nf-core-hic-methods-description":
order: -1000
- "nf-core-hic-summary":
+ software_versions:
order: -1001
+ "nf-core-hic-summary":
+ order: -1002
export_plots: true
diff --git a/assets/slackreport.json b/assets/slackreport.json
new file mode 100644
index 0000000000000000000000000000000000000000..043d02f27570da8e53dd7d3dd6d0a640cfa4636d
--- /dev/null
+++ b/assets/slackreport.json
@@ -0,0 +1,34 @@
+{
+ "attachments": [
+ {
+ "fallback": "Plain-text summary of the attachment.",
+ "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+ "author_name": "sanger-tol/readmapping v${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/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 6be15bd25d60d6901b2ff4154033e6271d9f3869..59af511a348b1c995da1fb70075f50e3a6ff5a51 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -10,7 +10,6 @@ import sys
from collections import Counter
from pathlib import Path
-
logger = logging.getLogger()
@@ -78,13 +77,15 @@ class RowChecker:
def _validate_sample(self, row):
"""Assert that the sample name exists and convert spaces to underscores."""
- assert len(row[self._sample_col]) > 0, "Sample input is required."
+ if len(row[self._sample_col]) <= 0:
+ raise AssertionError("Sample input is required.")
# Sanitize samples slightly.
row[self._sample_col] = row[self._sample_col].replace(" ", "_")
def _validate_first(self, row):
"""Assert that the first FASTQ entry is non-empty and has the right format."""
- assert len(row[self._first_col]) > 0, "At least the first FASTQ file is required."
+ if len(row[self._first_col]) <= 0:
+ raise AssertionError("At least the first FASTQ file is required.")
self._validate_fastq_format(row[self._first_col])
def _validate_second(self, row):
@@ -96,36 +97,36 @@ class RowChecker:
"""Assert that read pairs have the same file extension. Report pair status."""
if row[self._first_col] and row[self._second_col]:
row[self._single_col] = False
- assert (
- Path(row[self._first_col]).suffixes[-2:] == Path(row[self._second_col]).suffixes[-2:]
- ), "FASTQ pairs must have the same file extensions."
+ first_col_suffix = Path(row[self._first_col]).suffixes[-2:]
+ second_col_suffix = Path(row[self._second_col]).suffixes[-2:]
+ if first_col_suffix != second_col_suffix:
+ raise AssertionError("FASTQ pairs must have the same file extensions.")
else:
row[self._single_col] = True
def _validate_fastq_format(self, filename):
"""Assert that a given filename has one of the expected FASTQ extensions."""
- assert any(filename.endswith(extension) for extension in self.VALID_FORMATS), (
- f"The FASTQ file has an unrecognized extension: {filename}\n"
- f"It should be one of: {', '.join(self.VALID_FORMATS)}"
- )
+ if not any(filename.endswith(extension) for extension in self.VALID_FORMATS):
+ raise AssertionError(
+ f"The FASTQ file has an unrecognized extension: {filename}\n"
+ f"It should be one of: {', '.join(self.VALID_FORMATS)}"
+ )
def validate_unique_samples(self):
"""
Assert that the combination of sample name and FASTQ filename is unique.
- In addition to the validation, also rename the sample if more than one sample,
- FASTQ file combination exists.
+ In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the
+ number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment.
"""
- assert len(self._seen) == len(self.modified), "The pair of sample name and FASTQ must be unique."
- if len({pair[0] for pair in self._seen}) < len(self._seen):
- counts = Counter(pair[0] for pair in self._seen)
- seen = Counter()
- for row in self.modified:
- sample = row[self._sample_col]
- seen[sample] += 1
- #if counts[sample] > 1:
- # row[self._sample_col] = f"{sample}_T{seen[sample]}"
+ if len(self._seen) != len(self.modified):
+ raise AssertionError("The pair of sample name and FASTQ must be unique.")
+ seen = Counter()
+ for row in self.modified:
+ sample = row[self._sample_col]
+ seen[sample] += 1
+ row[self._sample_col] = f"{sample}_T{seen[sample]}"
def read_head(handle, num_lines=10):
@@ -157,7 +158,7 @@ def sniff_format(handle):
handle.seek(0)
sniffer = csv.Sniffer()
if not sniffer.has_header(peek):
- logger.critical(f"The given sample sheet does not appear to contain a header.")
+ logger.critical("The given sample sheet does not appear to contain a header.")
sys.exit(1)
dialect = sniffer.sniff(peek)
return dialect
@@ -195,7 +196,8 @@ def check_samplesheet(file_in, file_out):
reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
# Validate the existence of the expected header columns.
if not required_columns.issubset(reader.fieldnames):
- logger.critical(f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}.")
+ req_cols = ", ".join(required_columns)
+ logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
sys.exit(1)
# Validate each row.
checker = RowChecker()
diff --git a/conf/base.config b/conf/base.config
index e1895e3f5a6e7dfcc9b68b268225d7a8dd5376a7..6808dbe2205a3cbe53975d4d2d2ec2fbc1998ec7 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -24,6 +24,11 @@ process {
// If possible, it would be nice to keep the same label naming convention when
// adding in your local modules too.
// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+ withLabel:process_single {
+ cpus = { check_max( 1 , 'cpus' ) }
+ memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+ time = { check_max( 4.h * task.attempt, 'time' ) }
+ }
withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
diff --git a/docs/usage.md b/docs/usage.md
index 79d033b9ffd226a478b7848748803ee62d1400fe..159daa6bd15ec41ac0368264c84f8995ff42e654 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -10,7 +10,7 @@
You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
-```console
+```bash
--input '[path to samplesheet file]'
```
@@ -54,7 +54,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
The typical command for running the pipeline is as follows:
-```console
+```bash
nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
```
@@ -63,9 +63,9 @@ See below for more information about profiles.
Note that the pipeline will create the following files in your working directory:
-```console
+```bash
work # Directory containing the nextflow working files
-<OUTIDR> # Finished results in specified location (defined with --outdir)
+<OUTDIR> # Finished results in specified location (defined with --outdir)
.nextflow_log # Log file from Nextflow
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
```
@@ -74,7 +74,7 @@ work # Directory containing the nextflow working files
When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
-```console
+```bash
nextflow pull nf-core/hic
```
@@ -82,22 +82,9 @@ 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`.
-
-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.
+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.
-### Automatic resubmission
-
-Each step in the pipeline has a default set of requirements for number of CPUs,
-memory and time. For most of the steps in the pipeline, if the job exits with
-an error code of `143` (exceeded requested resources) it will automatically
-resubmit with higher requests (2 x original, then 3 x original). If it still
-fails after three times then the pipeline is stopped.
+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
@@ -109,7 +96,7 @@ fails after three times then the pipeline is stopped.
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.
@@ -127,10 +114,11 @@ 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`
@@ -143,9 +131,6 @@ installed and available on the `PATH`. This is _not_ recommended.
- 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`
@@ -196,8 +181,14 @@ 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.
@@ -216,7 +207,7 @@ 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`.
@@ -266,6 +257,14 @@ If you have any questions or issues please send us a message on
[Slack](https://nf-co.re/join/slack) on the
[`#configs` channel](https://nfcore.slack.com/channels/configs).
+## Azure Resource Requests
+
+To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
+We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
+
+Note that the choice of VM size depends on your quota and the overall workload during the analysis.
+For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
+
## Running in the background
Nextflow handles job submissions and supervises the running jobs.
@@ -287,7 +286,7 @@ large amount of memory.
We recommend adding the following line to your environment to limit this
(typically in `~/.bashrc` or `~./bash_profile`):
-```console
+```bash
NXF_OPTS='-Xms1g -Xmx4g'
```
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
old mode 100755
new mode 100644
index 28567bd70d63ebdae1340a22458cf8bc5a6fecf2..8d030f4e844bb87ca93fbe4f905e53a833b40840
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -21,19 +21,26 @@ class Utils {
}
// Check that all channels are present
- def required_channels = ['conda-forge', 'bioconda', 'defaults']
- def conda_check_failed = !required_channels.every { ch -> ch in channels }
+ // This channel list is ordered by required channel priority.
+ def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+ def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
// Check that they are in the right order
- conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
- conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+ def channel_priority_violation = false
+ def n = required_channels_in_order.size()
+ for (int i = 0; i < n - 1; i++) {
+ channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+ }
- if (conda_check_failed) {
+ if (channels_missing | channel_priority_violation) {
log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" There is a problem with your Conda configuration!\n\n" +
" You will need to set-up the conda-forge and bioconda channels correctly.\n" +
- " Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
- " NB: The order of the channels matters!\n" +
+ " Please refer to https://bioconda.github.io/\n" +
+ " The observed channel order is \n" +
+ " ${channels}\n" +
+ " but the following channel order is required:\n" +
+ " ${required_channels_in_order}\n" +
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
}
}
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
index b4755f41108622089151cf40d381d6e40b8e032b..3dea732db2bb9c05d5002920297d8d727efea9d0 100755
--- a/lib/WorkflowHic.groovy
+++ b/lib/WorkflowHic.groovy
@@ -2,6 +2,8 @@
// This file holds several functions specific to the workflow/hic.nf in the nf-core/hic pipeline
//
+import groovy.text.SimpleTemplateEngine
+
class WorkflowHic {
//
@@ -51,7 +53,22 @@ class WorkflowHic {
return yaml_file_text
}
- //
+ public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
+ // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+ def meta = [:]
+ meta.workflow = run_workflow.toMap()
+ meta["manifest_map"] = run_workflow.manifest.toMap()
+
+ meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
+ meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+ def methods_text = mqc_methods_yaml.text
+
+ def engine = new SimpleTemplateEngine()
+ def description_html = engine.createTemplate(methods_text).make(meta)
+
+ return description_html
+ }//
// Exit pipeline if incorrect --genome key provided
//
private static void genomeExistsError(params, log) {
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index fd70920b4cc9807708cac168f754d1ae661ab073..239d4fe7253d3a060bd99bff6b7842cdeb2891c8 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -18,7 +18,7 @@ class WorkflowMain {
}
//
- // Print help to screen if required
+ // Generate help string
//
public static String help(workflow, params, log) {
def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
@@ -31,7 +31,7 @@ class WorkflowMain {
}
//
- // Print parameter summary log to screen
+ // Generate parameter summary log string
//
public static String paramsSummaryLog(workflow, params, log) {
def summary_log = ''
@@ -52,19 +52,26 @@ class WorkflowMain {
System.exit(0)
}
- // Validate workflow parameters via the JSON schema
- if (params.validate_params) {
- NfcoreSchema.validateParameters(workflow, params, log)
+ // Print workflow version and exit on --version
+ if (params.version) {
+ String workflow_version = NfcoreTemplate.version(workflow)
+ log.info "${workflow.manifest.name} ${workflow_version}"
+ System.exit(0)
}
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
+ // Validate workflow parameters via the JSON schema
+ if (params.validate_params) {
+ NfcoreSchema.validateParameters(workflow, params, log)
+ }
+
// Check that a -profile or Nextflow config has been provided to run the pipeline
NfcoreTemplate.checkConfigProvided(workflow, log)
// Check that conda channels are set-up correctly
- if (params.enable_conda) {
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
Utils.checkCondaChannels(log)
}
@@ -77,17 +84,15 @@ class WorkflowMain {
System.exit(1)
}
}
-
//
// Get attribute from genome config file e.g. fasta
//
- public static String getGenomeAttribute(params, attribute) {
- def val = ''
+ public static Object getGenomeAttribute(params, attribute) {
if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
if (params.genomes[ params.genome ].containsKey(attribute)) {
- val = params.genomes[ params.genome ][ attribute ]
+ return params.genomes[ params.genome ][ attribute ]
}
}
- return val
+ return null
}
}
diff --git a/main.nf b/main.nf
index 82aaf0f200b77db6710472f821c715376d2e5668..dd564aa4e80652c1a21ba504c0564faddfb74bcd 100644
--- a/main.nf
+++ b/main.nf
@@ -4,6 +4,7 @@
nf-core/hic
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/hic
+
Website: https://nf-co.re/hic
Slack : https://nfcore.slack.com/channels/hic
----------------------------------------------------------------------------------------
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 31f62fa99c98fdf3938dd5a360c5d4e522479704..1624dfafe6425f07bbd15daf3b2735ea1187c0ec 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -1,7 +1,8 @@
process SAMPLESHEET_CHECK {
tag "$samplesheet"
+ label 'process_single'
- conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+ conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
'quay.io/biocontainers/python:3.8.3' }"
@@ -13,6 +14,9 @@ process SAMPLESHEET_CHECK {
path '*.csv' , emit: csv
path "versions.yml", emit: versions
+ when:
+ task.ext.when == null || task.ext.when
+
script: // This script is bundled with the pipeline, in nf-core/hic/bin/
"""
check_samplesheet.py \\
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index da03340857c4c90957c79c9f892030bc1bb397a3..a06f32b4aaa481be00f5f9b10fa44c4d2d16be9e 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -4,10 +4,18 @@
"""Provide functions to merge multiple versions.yml files."""
+<<<<<<< HEAD
import yaml
import platform
from textwrap import dedent
+=======
+import platform
+from textwrap import dedent
+
+import yaml
+
+>>>>>>> c5796cd967b920b736acba2ee60128d6ac0338db
def _make_versions_html(versions):
"""Generate a tabular HTML output of all versions for MultiQC."""
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..68f66bea74a65319549b9834af05cc9a38a1f30a
--- /dev/null
+++ b/modules/nf-core/multiqc/main.nf
@@ -0,0 +1,53 @@
+process MULTIQC {
+ label 'process_single'
+
+ conda "bioconda::multiqc=1.13"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+
+ input:
+ path multiqc_files, stageAs: "?/*"
+ path(multiqc_config)
+ path(extra_multiqc_config)
+ path(multiqc_logo)
+
+ output:
+ path "*multiqc_report.html", emit: report
+ path "*_data" , emit: data
+ path "*_plots" , optional:true, emit: plots
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def config = multiqc_config ? "--config $multiqc_config" : ''
+ def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+ """
+ multiqc \\
+ --force \\
+ $args \\
+ $config \\
+ $extra_config \\
+ .
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+ END_VERSIONS
+ """
+
+ stub:
+ """
+ touch multiqc_data
+ touch multiqc_plots
+ touch multiqc_report.html
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ebc29b279d565eb11d8923de0b87fd2fb14b1cbe
--- /dev/null
+++ b/modules/nf-core/multiqc/meta.yml
@@ -0,0 +1,55 @@
+name: MultiQC
+description: Aggregate results from bioinformatics analyses across many samples into a single report
+keywords:
+ - QC
+ - bioinformatics tools
+ - Beautiful stand-alone HTML report
+tools:
+ - multiqc:
+ description: |
+ MultiQC searches a given directory for analysis logs and compiles a HTML report.
+ It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+ homepage: https://multiqc.info/
+ documentation: https://multiqc.info/docs/
+ licence: ["GPL-3.0-or-later"]
+
+input:
+ - multiqc_files:
+ type: file
+ description: |
+ List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+ - multiqc_config:
+ type: file
+ description: Optional config yml for MultiQC
+ pattern: "*.{yml,yaml}"
+ - extra_multiqc_config:
+ type: file
+ description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
+ pattern: "*.{yml,yaml}"
+ - multiqc_logo:
+ type: file
+ description: Optional logo file for MultiQC
+ pattern: "*.{png}"
+
+output:
+ - report:
+ type: file
+ description: MultiQC report file
+ pattern: "multiqc_report.html"
+ - data:
+ type: dir
+ description: MultiQC data dir
+ pattern: "multiqc_data"
+ - plots:
+ type: file
+ description: Plots created by MultiQC
+ pattern: "*_data"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+authors:
+ - "@abhi18av"
+ - "@bunop"
+ - "@drpatelh"
+ - "@jfy133"
diff --git a/nextflow.config b/nextflow.config
index 18694f2a1905f69618b798b9a84af9ccdea9bd19..aad6d92ec7f5cbdd0555ad8d9bd8703cc3b533b2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,6 +12,7 @@ params {
// Input options
input = null
+
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
@@ -92,7 +93,9 @@ params {
// MultiQC options
multiqc_config = null
multiqc_title = null
+ multiqc_logo = null
max_multiqc_email_size = '25.MB'
+ multiqc_methods_description = null
// Boilerplate options
outdir = './results'
@@ -102,11 +105,13 @@ params {
email_on_fail = null
plaintext_email = false
monochrome_logs = false
+ hook_url = null
help = false
+ version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
- enable_conda = false
+
// Config options
custom_config_version = 'master'
@@ -116,6 +121,7 @@ params {
config_profile_url = null
config_profile_name = null
+
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
@@ -149,7 +155,16 @@ try {
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
- params.enable_conda = true
+ conda.enabled = true
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ mamba {
+ conda.enabled = true
+ conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
@@ -164,6 +179,9 @@ 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
@@ -193,10 +211,16 @@ profiles {
podman.enabled = false
shifter.enabled = false
}
+ gitpod {
+ executor.name = 'local'
+ executor.cpus = 16
+ executor.memory = 60.GB
+ }
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
+
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
@@ -204,6 +228,7 @@ if (!params.igenomes_ignore) {
params.genomes = [:]
}
+
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -238,12 +263,13 @@ 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 = ''
}
// Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ecc9df497f2ca3662468e6649ae602becd4a7542..96e9e09ebf0880d1494566c733fdc2e07129c21b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -433,6 +433,12 @@
"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",
@@ -470,12 +476,30 @@
"fa_icon": "fas fa-palette",
"hidden": true
},
+ "hook_url": {
+ "type": "string",
+ "description": "Incoming hook URL for messaging service",
+ "fa_icon": "fas fa-people-group",
+ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
+ "hidden": true
+ },
"multiqc_config": {
"type": "string",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
+ "multiqc_logo": {
+ "type": "string",
+ "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
+ "fa_icon": "fas fa-image",
+ "hidden": true
+ },
+ "multiqc_methods_description": {
+ "type": "string",
+ "description": "Custom MultiQC yaml file containing HTML including a methods description.",
+ "fa_icon": "fas fa-cog"
+ },
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
@@ -496,12 +520,6 @@
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
- },
- "enable_conda": {
- "type": "boolean",
- "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
- "hidden": true,
- "fa_icon": "fas fa-bacon"
}
}
}
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000000000000000000000000000000000..0d62beb6f970a40843767771cc66ee0df14b21ce
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,10 @@
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.black]
+line-length = 120
+target_version = ["py37", "py38", "py39", "py310"]
+
+[tool.isort]
+profile = "black"
+known_first_party = ["nf_core"]
+multi_line_output = 3
diff --git a/workflows/hic.nf b/workflows/hic.nf
index a58b89c57a3b19399c95a22a93a82eb330cecf72..3080227c58b6798fac494b0eddd9fe5695782e53 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -94,8 +94,10 @@ ch_map_res = ch_map_res.unique()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
+ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
+ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -128,20 +130,9 @@ include { TADS } from '../subworkflows/local/tads'
//
// MODULE: Installed directly from nf-core/modules
//
-
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
-include { FASTQC } from '../modules/nf-core/modules/fastqc/main'
-//include { MULTIQC } from '../modules/nf-core/modules/multiqc/main'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- CHANNELS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-Channel.fromPath( params.fasta )
- .ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
- .set { ch_fasta }
+include { FASTQC } from '../modules/nf-core/fastqc/main'
+include { MULTIQC } from '../modules/nf-core/multiqc/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -290,10 +281,13 @@ workflow HIC {
*/
workflow.onComplete {
- if (params.email || params.email_on_fail) {
- NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
- }
- NfcoreTemplate.summary(workflow, params, log)
+ if (params.email || params.email_on_fail) {
+ NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+ }
+ NfcoreTemplate.summary(workflow, params, log)
+ if (params.hook_url) {
+ NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
+ }
}
/*