diff --git a/.editorconfig b/.editorconfig
index b6b3190776e8d7f8894ed6484494018355814fc6..b78de6e655d209990fd9c1e70ae4882a9f0b4dff 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/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 9595a3a4100b3bb89694426519ca2570a2432e60..8da27af0eb9a6017271d057b39940493b3ac4bc4 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/chip
- [ ] 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/chipseq/tree/master/.github/CONTRIBUTING.md)
- - [ ] If necessary, also make a PR on the nf-core/chipseq _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/chipseq/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/chipseq _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/ci.yml b/.github/workflows/ci.yml
index 0596f36fc5d168f70629fc9b70b8610bdb521916..cf99db7f76ae62f9b4ddcdd2c3de6b30390a885b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,7 +10,6 @@ on:
env:
NXF_ANSI_LOG: false
- CAPSULE_LOG: none
jobs:
test:
@@ -20,27 +19,17 @@ 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:
+ - "21.10.3"
+ - "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- 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
# TODO nf-core: You can customise CI pipeline run tests as required
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 77358dee77fafceacab736de94ae79f2258a523f..8a5ce69b89514cf50a7efb930005ebc4f47074df 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -35,6 +35,36 @@ jobs:
- name: Run Prettier --check
run: prettier --check ${GITHUB_WORKSPACE}
+ PythonBlack:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+
+ - 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:
@@ -42,15 +72,11 @@ jobs:
uses: actions/checkout@v2
- 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
with:
- python-version: "3.6"
+ python-version: "3.7"
architecture: "x64"
- name: Install dependencies
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bcbe42c1b634cc4a8aab543a6073ee0e9cd49d97..ddd1153818ca6c06f3289320cf3694b0775f6e3d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## v1.3.0dev - [date]
+## v2.0.0 - [date]
Initial release of nf-core/chipseq, created with the [nf-core](https://nf-co.re/) template.
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000000000000000000000000000000000000..4533e2f28c1a4658d0f66cda65eb513cad8ab1c9
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,56 @@
+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: Ulysse Garcia
+ given-names: Maxime
+ - 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: Ulysse Garcia
+ given-names: Maxime
+ - 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 45ee3b4fceb9de1076a1ef729cb2cedfdfd904ff..095d129ce9f9eef6ef28b281964b227937d32107 100644
--- a/README.md
+++ b/README.md
@@ -1,19 +1,14 @@
#  
-[](https://github.com/nf-core/chipseq/actions?query=workflow%3A%22nf-core+CI%22)
-[](https://github.com/nf-core/chipseq/actions?query=workflow%3A%22nf-core+linting%22)
-[](https://nf-co.re/chipseq/results)
-[](https://doi.org/10.5281/zenodo.XXXXXXX)
+[](https://nf-co.re/chipseq/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://docs.conda.io/en/latest/)
+[](https://www.docker.com/)
+[](https://sylabs.io/docs/)
[](https://tower.nf/launch?pipeline=https://github.com/nf-core/chipseq)
-[](https://nfcore.slack.com/channels/chipseq)
-[](https://twitter.com/nf_core)
-[](https://www.youtube.com/c/nf-core)
+[](https://nfcore.slack.com/channels/chipseq)[](https://twitter.com/nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
@@ -25,7 +20,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
<!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
-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/chipseq/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/chipseq/results).
## Pipeline summary
@@ -42,7 +37,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
3. Download the pipeline and test it on a minimal dataset with a single command:
- ```console
+ ```bash
nextflow run nf-core/chipseq -profile test,YOURPROFILE --outdir <OUTDIR>
```
@@ -57,7 +52,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
<!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
- ```console
+ ```bash
nextflow run nf-core/chipseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
diff --git a/assets/email_template.txt b/assets/email_template.txt
index 6d35a69747238ca401b8596b9ff651a3e0adc71f..e1b7852605bfe226714fe7071b022c7757589bce 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -6,7 +6,6 @@
`._,._,'
nf-core/chipseq v${version}
----------------------------------------------------
-
Run Name: $runName
<% if (success){
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 3652c63c8b8f1f51035c3481c61ed1d5db8e8e1c..9a8b896239cc1ff4949a26090cd96a931491388b 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -11,7 +11,6 @@ import sys
from collections import Counter
from pathlib import Path
-
logger = logging.getLogger()
@@ -79,13 +78,15 @@ 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):
@@ -97,36 +98,34 @@ 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."
+ if Path(row[self._first_col]).suffixes[-2:] != Path(row[self._second_col]).suffixes[-2:]:
+ 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):
diff --git a/conf/base.config b/conf/base.config
index 8231c479600ced8e2ff57142bdc5ed4c86d0c26b..daf12c7c7c95012784ff4de442e00c95c9358936 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -26,6 +26,11 @@ process {
// adding in your local modules too.
// TODO nf-core: Customise requirements for specific processes.
// 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( 12.GB * task.attempt, 'memory' ) }
diff --git a/docs/images/nf-core-chipseq_logo_dark.png b/docs/images/nf-core-chipseq_logo_dark.png
index cf22a2e865ba247de7727c84ee2e990aa932803e..9f2b30100fd7ed5870367833ae6567d1dd97f407 100644
Binary files a/docs/images/nf-core-chipseq_logo_dark.png and b/docs/images/nf-core-chipseq_logo_dark.png differ
diff --git a/docs/usage.md b/docs/usage.md
index e6dc9daa9b2a93d75903121490c9336dad974aa2..997dfd2ce7916156d50d66e6764607cfbc37a88a 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -12,7 +12,7 @@
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]'
```
@@ -56,7 +56,7 @@ 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/chipseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
```
@@ -64,9 +64,9 @@ This will launch the pipeline with the `docker` configuration profile. See below
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.
```
@@ -75,7 +75,7 @@ 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/chipseq
```
@@ -251,6 +251,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo
In some cases, the Nextflow Java virtual machines can start to request a 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/WorkflowChipseq.groovy b/lib/WorkflowChipseq.groovy
index 547194f75a18dd576ab6c76d4b5cf89f66c55544..a5952af0cfd23882875cd8d47e5dd06b0b2841a4 100755
--- a/lib/WorkflowChipseq.groovy
+++ b/lib/WorkflowChipseq.groovy
@@ -10,6 +10,7 @@ class WorkflowChipseq {
public static void initialise(params, log) {
genomeExistsError(params, log)
+
if (!params.fasta) {
log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
System.exit(1)
@@ -41,9 +42,7 @@ class WorkflowChipseq {
yaml_file_text += "data: |\n"
yaml_file_text += "${summary_section}"
return yaml_file_text
- }
-
- //
+ }//
// Exit pipeline if incorrect --genome key provided
//
private static void genomeExistsError(params, log) {
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 0bf58e4358ebb17557bdf52a7ed3b306b47a2de5..904824ae27dc92a85f8c3af16f44b417fc724eda 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -59,6 +59,7 @@ class WorkflowMain {
}
// Print parameter summary log to screen
+
log.info paramsSummaryLog(workflow, params, log)
// Check that a -profile or Nextflow config has been provided to run the pipeline
@@ -78,17 +79,15 @@ 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 cf50b1183b11816e6748cd6ddcdc71d0f3cdd23c..d6adc85138b6af1b09347940870bee4edd7b03bd 100644
--- a/main.nf
+++ b/main.nf
@@ -4,7 +4,7 @@
nf-core/chipseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/chipseq
- Website: https://nf-co.re/chipseq
+Website: https://nf-co.re/chipseq
Slack : https://nfcore.slack.com/channels/chipseq
----------------------------------------------------------------------------------------
*/
diff --git a/modules.json b/modules.json
index 72584e8a490192db6db0dc7ae6425b339297c0d0..db8387141a39cf7f90ca60d148273a1c6ecb2f8d 100644
--- a/modules.json
+++ b/modules.json
@@ -3,14 +3,20 @@
"homePage": "https://github.com/nf-core/chipseq",
"repos": {
"nf-core/modules": {
- "custom/dumpsoftwareversions": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "fastqc": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "multiqc": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+ "git_url": "https://github.com/nf-core/modules.git",
+ "modules": {
+ "custom/dumpsoftwareversions": {
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
+ "branch": "master"
+ },
+ "fastqc": {
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
+ "branch": "master"
+ },
+ "multiqc": {
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
+ "branch": "master"
+ }
}
}
}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index d13903925467e97e353f0a4e6bcf9f6cdb8a3664..787bdb7b1b5a3564a74592275d34a3fa8d0f96d1 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -1,9 +1,10 @@
#!/usr/bin/env python
-import yaml
import platform
from textwrap import dedent
+import yaml
+
def _make_versions_html(versions):
html = [
@@ -58,11 +59,12 @@ versions_by_module = {}
for process, process_versions in versions_by_process.items():
module = process.split(":")[-1]
try:
- assert versions_by_module[module] == process_versions, (
- "We assume that software versions are the same between all modules. "
- "If you see this error-message it means you discovered an edge-case "
- "and should open an issue in nf-core/tools. "
- )
+ if versions_by_module[module] != process_versions:
+ raise AssertionError(
+ "We assume that software versions are the same between all modules. "
+ "If you see this error-message it means you discovered an edge-case "
+ "and should open an issue in nf-core/tools. "
+ )
except KeyError:
versions_by_module[module] = process_versions
diff --git a/nextflow.config b/nextflow.config
index 6c5ab6b95155947070ecf7dc3fdd2612aadb3407..08da317e869833d52775f45e006face465f06711 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,11 +13,11 @@ params {
// Input options
input = null
+
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
-
// MultiQC options
multiqc_config = null
multiqc_title = null
@@ -37,6 +37,7 @@ params {
schema_ignore_params = 'genomes'
enable_conda = false
+
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
@@ -45,6 +46,7 @@ params {
config_profile_url = null
config_profile_name = null
+
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
@@ -72,6 +74,7 @@ try {
// }
+
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
@@ -82,6 +85,15 @@ profiles {
shifter.enabled = false
charliecloud.enabled = false
}
+ mamba {
+ params.enable_conda = true
+ conda.useMamba = true
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
docker {
docker.enabled = true
docker.userEmulation = true
@@ -119,10 +131,16 @@ 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'
@@ -130,6 +148,7 @@ 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.
@@ -169,7 +188,7 @@ manifest {
description = 'ChIP-seq peak-calling and differential analysis pipeline.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
- version = '1.3.0dev'
+ version = '2.0.0'
}
// Load modules.config for DSL2 module specific options