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Merge branch 'dev' into json-schema

This commit is contained in:
James Fellows Yates 2022-08-31 12:55:49 +02:00
commit 3eb136ec3c
16 changed files with 146 additions and 63 deletions

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@ -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

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@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/taxp
- [ ] 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/taxprofiler/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/taxprofiler _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/taxprofiler/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/taxprofiler _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.

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@ -10,7 +10,6 @@ on:
env:
NXF_ANSI_LOG: false
CAPSULE_LOG: none
jobs:
test:
@ -20,14 +19,9 @@ 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"
parameters:
- "--perform_longread_qc false"
- "--perform_shortread_qc false"
@ -48,14 +42,9 @@ jobs:
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: Show current locale
run: locale

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@ -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

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@ -6,5 +6,5 @@ results/
.DS_Store
testing/
testing*
tests/
*.pyc
tests/

56
CITATION.cff Normal file
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@ -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

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@ -1,19 +1,14 @@
# ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_dark.png#gh-dark-mode-only)
[![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+CI%22)
[![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+linting%22)
[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)
[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/taxprofiler)
[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?logo=slack)](https://nfcore.slack.com/channels/taxprofiler)
[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](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/taxprofiler/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/taxprofiler/results).
## Pipeline summary
@ -59,7 +54,7 @@ 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/taxprofiler -profile test,YOURPROFILE --outdir <OUTDIR>
```

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@ -6,7 +6,6 @@
`._,._,'
nf-core/taxprofiler v${version}
----------------------------------------------------
Run Name: $runName
<% if (success){

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@ -6,7 +6,6 @@ import sys
import errno
import argparse
def parse_args(args=None):
Description = (
"Reformat nf-core/taxprofiler samplesheet file and check its contents."
@ -18,7 +17,6 @@ def parse_args(args=None):
parser.add_argument("FILE_OUT", help="Output file.")
return parser.parse_args(args)
def make_dir(path):
if len(path) > 0:
try:
@ -27,7 +25,6 @@ def make_dir(path):
if exception.errno != errno.EEXIST:
raise exception
def print_error(error, context="Line", context_str=""):
error_str = "ERROR: Please check samplesheet -> {}".format(error)
if context != "" and context_str != "":
@ -37,7 +34,6 @@ def print_error(error, context="Line", context_str=""):
print(error_str)
sys.exit(1)
def check_samplesheet(file_in, file_out):
"""
This function checks that the samplesheet follows the following structure:

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@ -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' ) }

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@ -154,7 +154,7 @@ 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
<OUTDIR> # Finished results in specified location (defined with --outdir)
.nextflow_log # Log file from Nextflow
@ -231,7 +231,7 @@ nf-core/taxprofiler uses MALT 0.4.1, which is a compatively old version. However
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/taxprofiler
```
@ -407,6 +407,6 @@ 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'
```

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@ -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
}
}

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@ -42,9 +42,7 @@ class WorkflowTaxprofiler {
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) {

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@ -4,7 +4,7 @@
nf-core/taxprofiler
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/taxprofiler
Website: https://nf-co.re/taxprofiler
Website: https://nf-co.re/taxprofiler
Slack : https://nfcore.slack.com/channels/taxprofiler
----------------------------------------------------------------------------------------
*/

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@ -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

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@ -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,fasta'
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'
@ -157,6 +159,7 @@ try {
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
@ -167,6 +170,15 @@ 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
@ -204,6 +216,11 @@ 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' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
@ -212,6 +229,7 @@ profiles {
test_motus { includeConfig 'conf/test_motus.config' }
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
@ -220,6 +238,7 @@ 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.