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Commit 44b7a17b authored by nservant's avatar nservant
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Merged vanilla TEMPLATE branch into main pipeline

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.github/CONTRIBUTING.md
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...@@ -6,7 +6,9 @@ We try to manage the required tasks for nf-core/hic using GitHub issues, you pro ...@@ -6,7 +6,9 @@ We try to manage the required tasks for nf-core/hic using GitHub issues, you pro
However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)
> If you need help using or modifying nf-core/hic then the best place to go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/nf-core/Lobby > If you need help using or modifying nf-core/hic then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
## Contribution workflow ## Contribution workflow
If you'd like to write some code for nf-core/hic, the standard workflow If you'd like to write some code for nf-core/hic, the standard workflow
...@@ -42,4 +44,4 @@ If there are any failures then the automated tests fail. ...@@ -42,4 +44,4 @@ If there are any failures then the automated tests fail.
These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code. These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.
## Getting help ## Getting help
For further information/help, please consult the [nf-core/hic documentation](https://github.com/nf-core/hic#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/nf-core/Lobby) For further information/help, please consult the [nf-core/hic documentation](https://github.com/nf-core/hic#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
.github/markdownlint.yml 0 → 100644
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# Markdownlint configuration file
default: true,
line-length: false
no-multiple-blanks: 0
blanks-around-headers: false
blanks-around-lists: false
header-increment: false
no-duplicate-header:
siblings_only: true
.gitignore
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...@@ -4,3 +4,4 @@ data/ ...@@ -4,3 +4,4 @@ data/
results/ results/
.DS_Store .DS_Store
tests/test_data tests/test_data
*.pyc
.travis.yml
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...@@ -13,6 +13,7 @@ before_install: ...@@ -13,6 +13,7 @@ before_install:
# Pull the docker image first so the test doesn't wait for this # Pull the docker image first so the test doesn't wait for this
- docker pull nfcore/hic:dev - docker pull nfcore/hic:dev
# Fake the tag locally so that the pipeline runs properly # Fake the tag locally so that the pipeline runs properly
# Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
- docker tag nfcore/hic:dev nfcore/hic:dev - docker tag nfcore/hic:dev nfcore/hic:dev
install: install:
...@@ -25,12 +26,17 @@ install: ...@@ -25,12 +26,17 @@ install:
- pip install nf-core - pip install nf-core
# Reset # Reset
- mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
# Install markdownlint-cli
- sudo apt-get install npm && npm install -g markdownlint-cli
env: env:
- NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
- NXF_VER='' # Plus: get the latest NF version and check that it works
script: script:
# Lint the pipeline code # Lint the pipeline code
- nf-core lint ${TRAVIS_BUILD_DIR} - nf-core lint ${TRAVIS_BUILD_DIR}
# Lint the documentation
- markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
# Run the pipeline with the test profile # Run the pipeline with the test profile
- nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
CODE_OF_CONDUCT.md
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...@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe ...@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
## Enforcement ## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on the [Gitter channel](https://gitter.im/nf-core/Lobby). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-core-invite.herokuapp.com/). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
......
README.md
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# ![nf-core/hic](docs/images/nfcore-hic_logo.png) # nf-core/hic
**Analysis of Chromosome Conformation Capture data (Hi-C)** **Analysis of Chromosome Conformation Capture data (Hi-C)**.
[![Build Status](https://travis-ci.org/nf-core/hic.svg?branch=master)](https://travis-ci.org/nf-core/hic) [![Build Status](https://travis-ci.com/nf-core/hic.svg?branch=master)](https://travis-ci.com/nf-core/hic)
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/) [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
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assets/email_template.txt
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...@@ -17,23 +17,6 @@ ${errorReport} ...@@ -17,23 +17,6 @@ ${errorReport}
} %> } %>
<% if (!success){
out << """####################################################
## nf-core/hic execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
The full error message was:
${errorReport}
"""
} else {
out << "## nf-core/hic execution completed successfully! ##"
}
%>
The workflow was completed at $dateComplete (duration: $duration) The workflow was completed at $dateComplete (duration: $duration)
The command used to launch the workflow was as follows: The command used to launch the workflow was as follows:
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assets/multiqc_config.yaml 0 → 100644
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report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://github.com/nf-core/hic" target="_blank">documentation</a>.
report_section_order:
nf-core/hic-software-versions:
order: -1000
export_plots: true
assets/sendmail_template.txt
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To: $email To: $email
Subject: $subject Subject: $subject
Mime-Version: 1.0 Mime-Version: 1.0
Content-Type: multipart/related;boundary="nfmimeboundary" Content-Type: multipart/related;boundary="nfcoremimeboundary"
--nfmimeboundary --nfcoremimeboundary
Content-Type: text/html; charset=utf-8 Content-Type: text/html; charset=utf-8
$email_html $email_html
--nfmimeboundary-- <%
if (mqcFile){
def mqcFileObj = new File("$mqcFile")
if (mqcFileObj.length() < mqcMaxSize){
out << """
--nfcoremimeboundary
Content-Type: text/html; name=\"multiqc_report\"
Content-Transfer-Encoding: base64
Content-ID: <mqcreport>
Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
${mqcFileObj.
bytes.
encodeBase64().
toString().
tokenize( '\n' )*.
toList()*.
collate( 76 )*.
collect { it.join() }.
flatten().
join( '\n' )}
"""
}}
%>
--nfcoremimeboundary--
bin/scrape_software_versions.py
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...@@ -7,10 +7,14 @@ import re ...@@ -7,10 +7,14 @@ import re
regexes = { regexes = {
'nf-core/hic': ['v_pipeline.txt', r"(\S+)"], 'nf-core/hic': ['v_pipeline.txt', r"(\S+)"],
'Nextflow': ['v_nextflow.txt', r"(\S+)"], 'Nextflow': ['v_nextflow.txt', r"(\S+)"],
'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
} }
results = OrderedDict() results = OrderedDict()
results['nf-core/hic'] = '<span style="color:#999999;\">N/A</span>' results['nf-core/hic'] = '<span style="color:#999999;\">N/A</span>'
results['Nextflow'] = '<span style="color:#999999;\">N/A</span>' results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
results['FastQC'] = '<span style="color:#999999;\">N/A</span>'
results['MultiQC'] = '<span style="color:#999999;\">N/A</span>'
# Search each file using its regex # Search each file using its regex
for k, v in regexes.items(): for k, v in regexes.items():
...@@ -20,9 +24,14 @@ for k, v in regexes.items(): ...@@ -20,9 +24,14 @@ for k, v in regexes.items():
if match: if match:
results[k] = "v{}".format(match.group(1)) results[k] = "v{}".format(match.group(1))
# Remove software set to false in results
for k in results:
if not results[k]:
del(results[k])
# Dump to YAML # Dump to YAML
print (''' print ('''
id: 'nf-core/hic-software-versions' id: 'software_versions'
section_name: 'nf-core/hic Software Versions' section_name: 'nf-core/hic Software Versions'
section_href: 'https://github.com/nf-core/hic' section_href: 'https://github.com/nf-core/hic'
plot_type: 'html' plot_type: 'html'
...@@ -31,5 +40,10 @@ data: | ...@@ -31,5 +40,10 @@ data: |
<dl class="dl-horizontal"> <dl class="dl-horizontal">
''') ''')
for k,v in results.items(): for k,v in results.items():
print(" <dt>{}</dt><dd>{}</dd>".format(k,v)) print(" <dt>{}</dt><dd><samp>{}</samp></dd>".format(k,v))
print (" </dl>") print (" </dl>")
# Write out regexes as csv file:
with open('software_versions.csv', 'w') as f:
for k,v in results.items():
f.write("{}\t{}\n".format(k,v))
conf/awsbatch.config
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/* /*
* ------------------------------------------------- * -------------------------------------------------
* Nextflow config file for AWS Batch * Nextflow config file for running on AWS batch
* ------------------------------------------------- * -------------------------------------------------
* Imported under the 'awsbatch' Nextflow profile in nextflow.config * Base config needed for running with -profile awsbatch
* Uses docker for software depedencies automagically, so not specified here.
*/ */
params {
config_profile_name = 'AWSBATCH'
config_profile_description = 'AWSBATCH Cloud Profile'
config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'https://aws.amazon.com/de/batch/'
}
aws.region = params.awsregion aws.region = params.awsregion
process.executor = 'awsbatch' process.executor = 'awsbatch'
......
conf/base.config
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/* /*
* ------------------------------------------------- * -------------------------------------------------
* Nextflow base config file * nf-core/hic Nextflow base config file
* ------------------------------------------------- * -------------------------------------------------
* A 'blank slate' config file, appropriate for general * A 'blank slate' config file, appropriate for general
* use on most high performace compute environments. * use on most high performace compute environments.
...@@ -11,13 +11,12 @@ ...@@ -11,13 +11,12 @@
process { process {
container = process.container // TODO nf-core: Check the defaults for all processes
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) } time = { check_max( 2.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'terminate' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 1 maxRetries = 1
maxErrors = '-1' maxErrors = '-1'
...@@ -25,7 +24,7 @@ process { ...@@ -25,7 +24,7 @@ process {
withName:makeBowtie2Index { withName:makeBowtie2Index {
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 10.GB * task.attempt, 'memory' ) } memory = { check_max( 10.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) } time = { check_max( 12.h * task.attempt, 'time' ) }
} }
withName:bowtie2_end_to_end { withName:bowtie2_end_to_end {
cpus = { check_max( 4, 'cpus' ) } cpus = { check_max( 4, 'cpus' ) }
......
conf/igenomes.config
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...@@ -60,7 +60,7 @@ params { ...@@ -60,7 +60,7 @@ params {
} }
'Gm01' { 'Gm01' {
fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/genome" bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/genome"
} }
'Mmul_1' { 'Mmul_1' {
fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
...@@ -96,7 +96,7 @@ params { ...@@ -96,7 +96,7 @@ params {
} }
'AGPv3' { 'AGPv3' {
fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/genome" bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/genome"
} }
} }
} }
conf/test.config
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...@@ -16,7 +16,7 @@ params { ...@@ -16,7 +16,7 @@ params {
max_cpus = 2 max_cpus = 2
max_memory = 4.GB max_memory = 4.GB
max_time = 1.h max_time = 1.h
// Input data // Input data
readPaths = [ readPaths = [
['SRR4292758_00', ['https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz']] ['SRR4292758_00', ['https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz']]
...@@ -31,4 +31,3 @@ params { ...@@ -31,4 +31,3 @@ params {
// Options // Options
skip_cool = true skip_cool = true
} }
docs/output.md
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...@@ -26,7 +26,7 @@ Singletons are discarded, and multi-hits are filtered according to the configura ...@@ -26,7 +26,7 @@ Singletons are discarded, and multi-hits are filtered according to the configura
Note that if the `--dnase` mode is activated, HiC-Pro will skip the second mapping step. Note that if the `--dnase` mode is activated, HiC-Pro will skip the second mapping step.
**Output directory: `results/mapping`** **Output directory: `results/mapping`**
* `*bwt2pairs.bam` - final BAM file with aligned paired data * `*bwt2pairs.bam` - final BAM file with aligned paired data
* `*.pairstat` - mapping statistics * `*.pairstat` - mapping statistics
...@@ -50,7 +50,7 @@ Invalid pairs are classified as follow: ...@@ -50,7 +50,7 @@ Invalid pairs are classified as follow:
* Dangling end, i.e. unligated fragments (both reads mapped on the same restriction fragment) * Dangling end, i.e. unligated fragments (both reads mapped on the same restriction fragment)
* Self circles, i.e. fragments ligated on themselves (both reads mapped on the same restriction fragment in inverted orientation) * Self circles, i.e. fragments ligated on themselves (both reads mapped on the same restriction fragment in inverted orientation)
* Religation, i.e. ligation of juxtaposed fragments * Religation, i.e. ligation of juxtaposed fragments
* Filtered pairs, i.e. any pairs that do not match the filtering criteria on inserts size, restriction fragments size * Filtered pairs, i.e. any pairs that do not match the filtering criteria on inserts size, restriction fragments size
* Dumped pairs, i.e. any pairs for which we were not able to reconstruct the ligation product. * Dumped pairs, i.e. any pairs for which we were not able to reconstruct the ligation product.
Only valid pairs involving two different restriction fragments are used to build the contact maps. Only valid pairs involving two different restriction fragments are used to build the contact maps.
...@@ -59,7 +59,7 @@ Duplicated valid pairs associated to PCR artefacts are discarded (see `--rm_dup` ...@@ -59,7 +59,7 @@ Duplicated valid pairs associated to PCR artefacts are discarded (see `--rm_dup`
In case of Hi-C protocols that do not require a restriction enzyme such as DNase Hi-C or micro Hi-C, the assignment to a restriction is not possible (see `--dnase`). In case of Hi-C protocols that do not require a restriction enzyme such as DNase Hi-C or micro Hi-C, the assignment to a restriction is not possible (see `--dnase`).
Short range interactions that are likely to be spurious ligation products can thus be discarded using the `--min_cis_dist` parameter. Short range interactions that are likely to be spurious ligation products can thus be discarded using the `--min_cis_dist` parameter.
* `*.validPairs` - List of valid ligation products * `*.validPairs` - List of valid ligation products
* `*RSstat` - Statitics of number of read pairs falling in each category * `*RSstat` - Statitics of number of read pairs falling in each category
The validPairs are stored using a simple tab-delimited text format ; The validPairs are stored using a simple tab-delimited text format ;
...@@ -124,4 +124,4 @@ The pipeline has special steps which allow the software versions used to be repo ...@@ -124,4 +124,4 @@ The pipeline has special steps which allow the software versions used to be repo
* `Project_multiqc_data/` * `Project_multiqc_data/`
* Directory containing parsed statistics from the different tools used in the pipeline * Directory containing parsed statistics from the different tools used in the pipeline
For more information about how to use MultiQC reports, see http://multiqc.info For more information about how to use MultiQC reports, see [http://multiqc.info](http://multiqc.info)
docs/usage.md
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...@@ -121,21 +121,22 @@ Use this parameter to choose a configuration profile. Profiles can give configur ...@@ -121,21 +121,22 @@ Use this parameter to choose a configuration profile. Profiles can give configur
If `-profile` is not specified at all the pipeline will be run locally and expects all software to be installed and available on the `PATH`. If `-profile` is not specified at all the pipeline will be run locally and expects all software to be installed and available on the `PATH`.
* `awsbatch` * `awsbatch`
* A generic configuration profile to be used with AWS Batch. * A generic configuration profile to be used with AWS Batch.
* `conda` * `conda`
* A generic configuration profile to be used with [conda](https://conda.io/docs/) * A generic configuration profile to be used with [conda](https://conda.io/docs/)
* Pulls most software from [Bioconda](https://bioconda.github.io/) * Pulls most software from [Bioconda](https://bioconda.github.io/)
* `docker` * `docker`
* A generic configuration profile to be used with [Docker](http://docker.com/) * A generic configuration profile to be used with [Docker](http://docker.com/)
* Pulls software from dockerhub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/) * Pulls software from dockerhub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/)
* `singularity` * `singularity`
* A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/) * A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/)
* Pulls software from singularity-hub * Pulls software from DockerHub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/)
* `test` * `test`
* A profile with a complete configuration for automated testing * A profile with a complete configuration for automated testing
* Includes links to test data so needs no other parameters * Includes links to test data so needs no other parameters
<!-- TODO nf-core: Document required command line parameters --> <!-- TODO nf-core: Document required command line parameters -->
### `--reads` ### `--reads`
Use this to specify the location of your input FastQ files. For example: Use this to specify the location of your input FastQ files. For example:
......
environment.yml
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# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-hic-1.0dev name: nf-core-hic-1.0dev
channels: channels:
- conda-forge - conda-forge
...@@ -16,4 +18,4 @@ dependencies: ...@@ -16,4 +18,4 @@ dependencies:
- samtools=1.7 - samtools=1.7
- multiqc=1.6 - multiqc=1.6
- pip: - pip:
- iced==0.4.2 - iced==0.4.2
\ No newline at end of file
main.nf
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...@@ -11,19 +11,9 @@ ...@@ -11,19 +11,9 @@
def helpMessage() { def helpMessage() {
// TODO nf-core: Add to this help message with new command line parameters
log.info nfcoreHeader()
log.info""" log.info"""
=======================================================
,--./,-.
___ __ __ __ ___ /,-._.--~\'
|\\ | |__ __ / ` / \\ |__) |__ } {
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
`._,._,\'
nf-core/hic v${workflow.manifest.version}
=======================================================
This pipeline is a Nextflow version of the HiC-Pro pipeline for Hi-C data processing.
See https://github.com/nservant/HiC-Pro for details.
Usage: Usage:
...@@ -107,7 +97,7 @@ if (!params.dnase && !params.ligation_site) { ...@@ -107,7 +97,7 @@ if (!params.dnase && !params.ligation_site) {
} }
// Reference index path configuration // Reference index path configuration
params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
...@@ -118,22 +108,21 @@ if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){ ...@@ -118,22 +108,21 @@ if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
custom_runName = workflow.runName custom_runName = workflow.runName
} }
if( workflow.profile == 'awsbatch') { if( workflow.profile == 'awsbatch') {
// AWSBatch sanity checking // AWSBatch sanity checking
if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
if (!workflow.workDir.startsWith('s3') || !params.outdir.startsWith('s3')) exit 1, "Specify S3 URLs for workDir and outdir parameters on AWSBatch!" // Check outdir paths to be S3 buckets if running on AWSBatch
// Check workDir/outdir paths to be S3 buckets if running on AWSBatch
// related: https://github.com/nextflow-io/nextflow/issues/813 // related: https://github.com/nextflow-io/nextflow/issues/813
if (!workflow.workDir.startsWith('s3:') || !params.outdir.startsWith('s3:')) exit 1, "Workdir or Outdir not on S3 - specify S3 Buckets for each to run on AWSBatch!" if (!params.outdir.startsWith('s3:')) exit 1, "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
// Prevent trace files to be stored on S3 since S3 does not support rolling files.
if (workflow.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
} }
// Stage config files // Stage config files
ch_multiqc_config = Channel.fromPath(params.multiqc_config) ch_multiqc_config = Channel.fromPath(params.multiqc_config)
ch_output_docs = Channel.fromPath("$baseDir/docs/output.md") ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
/********************************************************** /**********************************************************
* SET UP CHANNELS * SET UP CHANNELS
*/ */
...@@ -185,7 +174,7 @@ if ( params.bwt2_index ){ ...@@ -185,7 +174,7 @@ if ( params.bwt2_index ){
Channel.fromPath( bwt2_dir , checkIfExists: true) Channel.fromPath( bwt2_dir , checkIfExists: true)
.ifEmpty { exit 1, "Genome index: Provided index not found: ${params.bwt2_index}" } .ifEmpty { exit 1, "Genome index: Provided index not found: ${params.bwt2_index}" }
.into { bwt2_index_end2end; bwt2_index_trim } .into { bwt2_index_end2end; bwt2_index_trim }
} }
else if ( params.fasta ) { else if ( params.fasta ) {
lastPath = params.fasta.lastIndexOf(File.separator) lastPath = params.fasta.lastIndexOf(File.separator)
...@@ -199,7 +188,6 @@ else { ...@@ -199,7 +188,6 @@ else {
exit 1, "No reference genome specified!" exit 1, "No reference genome specified!"
} }
// Chromosome size // Chromosome size
if ( params.chromosome_size ){ if ( params.chromosome_size ){
...@@ -241,20 +229,10 @@ ch_output_docs = Channel.fromPath("$baseDir/docs/output.md") ...@@ -241,20 +229,10 @@ ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
*/ */
// Header log info // Header log info
log.info """======================================================= log.info nfcoreHeader()
,--./,-.
___ __ __ __ ___ /,-._.--~\'
|\\ | |__ __ / ` / \\ |__) |__ } {
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
`._,._,\'
nf-core/hic v${workflow.manifest.version}"
======================================================="""
def summary = [:] def summary = [:]
summary['Pipeline Name'] = 'nf-core/hic' if(workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Pipeline Version'] = workflow.manifest.version
summary['Run Name'] = custom_runName ?: workflow.runName summary['Run Name'] = custom_runName ?: workflow.runName
summary['Reads'] = params.reads summary['Reads'] = params.reads
summary['splitFastq'] = params.splitFastq summary['splitFastq'] = params.splitFastq
summary['Fasta Ref'] = params.fasta summary['Fasta Ref'] = params.fasta
...@@ -269,7 +247,7 @@ summary['Max Time'] = params.max_time ...@@ -269,7 +247,7 @@ summary['Max Time'] = params.max_time
summary['Output dir'] = params.outdir summary['Output dir'] = params.outdir
summary['Working dir'] = workflow.workDir summary['Working dir'] = workflow.workDir
summary['Container Engine'] = workflow.containerEngine summary['Container Engine'] = workflow.containerEngine
if(workflow.containerEngine) if(workflow.containerEngine)
summary['Container'] = workflow.container summary['Container'] = workflow.container
summary['Current home'] = "$HOME" summary['Current home'] = "$HOME"
summary['Current user'] = "$USER" summary['Current user'] = "$USER"
...@@ -282,10 +260,19 @@ if(workflow.profile == 'awsbatch'){ ...@@ -282,10 +260,19 @@ if(workflow.profile == 'awsbatch'){
summary['AWS Region'] = params.awsregion summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue summary['AWS Queue'] = params.awsqueue
} }
if(params.email) summary['E-mail Address'] = params.email summary['Config Profile'] = workflow.profile
log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n") if(params.config_profile_description) summary['Config Description'] = params.config_profile_description
log.info "=========================================" if(params.config_profile_contact) summary['Config Contact'] = params.config_profile_contact
if(params.config_profile_url) summary['Config URL'] = params.config_profile_url
if(params.email) {
summary['E-mail Address'] = params.email
summary['MultiQC maxsize'] = params.maxMultiqcEmailFileSize
}
log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
log.info "\033[2m----------------------------------------------------\033[0m"
// Check the hostnames against configured profiles
checkHostname()
def create_workflow_summary(summary) { def create_workflow_summary(summary) {
def yaml_file = workDir.resolve('workflow_summary_mqc.yaml') def yaml_file = workDir.resolve('workflow_summary_mqc.yaml')
...@@ -309,19 +296,25 @@ ${summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style ...@@ -309,19 +296,25 @@ ${summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style
* Parse software version numbers * Parse software version numbers
*/ */
process get_software_versions { process get_software_versions {
publishDir "${params.outdir}/pipeline_info", mode: 'copy',
saveAs: {filename ->
if (filename.indexOf(".csv") > 0) filename
else null
}
output: output:
file 'software_versions_mqc.yaml' into software_versions_yaml file 'software_versions_mqc.yaml' into software_versions_yaml
file "software_versions.csv"
script: script:
""" """
echo $workflow.manifest.version > v_pipeline.txt echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt echo $workflow.nextflow.version > v_nextflow.txt
bowtie2 --version > v_bowtie2.txt bowtie2 --version > v_bowtie2.txt
python --version > v_python.txt python --version > v_python.txt
samtools --version > v_samtools.txt samtools --version > v_samtools.txt
scrape_software_versions.py > software_versions_mqc.yaml scrape_software_versions.py &> software_versions_mqc.yaml
""" """
} }
...@@ -362,13 +355,13 @@ if(!params.chromosome_size && params.fasta){ ...@@ -362,13 +355,13 @@ if(!params.chromosome_size && params.fasta){
file fasta from fasta_for_chromsize file fasta from fasta_for_chromsize
output: output:
file "*.size" into chromosome_size, chromosome_size_cool file "*.size" into chromosome_size, chromosome_size_cool
script: script:
""" """
samtools faidx ${fasta} samtools faidx ${fasta}
cut -f1,2 ${fasta}.fai > chrom.size cut -f1,2 ${fasta}.fai > chrom.size
""" """
} }
} }
...@@ -407,7 +400,7 @@ process bowtie2_end_to_end { ...@@ -407,7 +400,7 @@ process bowtie2_end_to_end {
input: input:
set val(sample), file(reads) from raw_reads set val(sample), file(reads) from raw_reads
file index from bwt2_index_end2end.collect() file index from bwt2_index_end2end.collect()
output: output:
set val(prefix), file("${prefix}_unmap.fastq") into unmapped_end_to_end set val(prefix), file("${prefix}_unmap.fastq") into unmapped_end_to_end
set val(prefix), file("${prefix}.bam") into end_to_end_bam set val(prefix), file("${prefix}.bam") into end_to_end_bam
...@@ -415,7 +408,7 @@ process bowtie2_end_to_end { ...@@ -415,7 +408,7 @@ process bowtie2_end_to_end {
script: script:
prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/ prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
def bwt2_opts = params.bwt2_opts_end2end def bwt2_opts = params.bwt2_opts_end2end
if (!params.dnase){ if (!params.dnase){
""" """
bowtie2 --rg-id BMG --rg SM:${prefix} \\ bowtie2 --rg-id BMG --rg SM:${prefix} \\
...@@ -506,13 +499,13 @@ if (!params.dnase){ ...@@ -506,13 +499,13 @@ if (!params.dnase){
""" """
samtools merge -@ ${task.cpus} \\ samtools merge -@ ${task.cpus} \\
-f ${prefix}_bwt2merged.bam \\ -f ${prefix}_bwt2merged.bam \\
${bam1} ${bam2} ${bam1} ${bam2}
samtools sort -@ ${task.cpus} -m 800M \\ samtools sort -@ ${task.cpus} -m 800M \\
-n -T /tmp/ \\ -n -T /tmp/ \\
-o ${prefix}_bwt2merged.sorted.bam \\ -o ${prefix}_bwt2merged.sorted.bam \\
${prefix}_bwt2merged.bam ${prefix}_bwt2merged.bam
mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
echo "## ${prefix}" > ${prefix}.mapstat echo "## ${prefix}" > ${prefix}.mapstat
...@@ -557,13 +550,11 @@ if (!params.dnase){ ...@@ -557,13 +550,11 @@ if (!params.dnase){
} }
} }
process combine_mapped_files{ process combine_mapped_files{
tag "$sample = $r1_prefix + $r2_prefix" tag "$sample = $r1_prefix + $r2_prefix"
publishDir "${params.outdir}/mapping", mode: 'copy', publishDir "${params.outdir}/mapping", mode: 'copy',
saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"} saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"}
input: input:
set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple() set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple()
...@@ -577,7 +568,7 @@ process combine_mapped_files{ ...@@ -577,7 +568,7 @@ process combine_mapped_files{
r2_bam = aligned_bam[1] r2_bam = aligned_bam[1]
r2_prefix = r2_bam.toString() - ~/_bwt2merged.bam$/ r2_prefix = r2_bam.toString() - ~/_bwt2merged.bam$/
oname = sample.toString() - ~/(\.[0-9]+)$/ oname = sample.toString() - ~/(\.[0-9]+)$/
def opts = "-t" def opts = "-t"
opts = params.rm_singleton ? "${opts}" : "--single ${opts}" opts = params.rm_singleton ? "${opts}" : "--single ${opts}"
opts = params.rm_multi ? "${opts}" : "--multi ${opts}" opts = params.rm_multi ? "${opts}" : "--multi ${opts}"
...@@ -596,7 +587,7 @@ if (!params.dnase){ ...@@ -596,7 +587,7 @@ if (!params.dnase){
process get_valid_interaction{ process get_valid_interaction{
tag "$sample" tag "$sample"
publishDir "${params.outdir}/hic_results/data", mode: 'copy', publishDir "${params.outdir}/hic_results/data", mode: 'copy',
saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$filename" : "$filename"} saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$filename" : "$filename"}
input: input:
set val(sample), file(pe_bam) from paired_bam set val(sample), file(pe_bam) from paired_bam
...@@ -607,7 +598,7 @@ if (!params.dnase){ ...@@ -607,7 +598,7 @@ if (!params.dnase){
set val(sample), file("*.validPairs") into valid_pairs_4cool set val(sample), file("*.validPairs") into valid_pairs_4cool
set val(sample), file("*RSstat") into all_rsstat set val(sample), file("*RSstat") into all_rsstat
script: script:
if (params.splitFastq){ if (params.splitFastq){
sample = sample.toString() - ~/(\.[0-9]+)$/ sample = sample.toString() - ~/(\.[0-9]+)$/
} }
...@@ -628,17 +619,17 @@ else{ ...@@ -628,17 +619,17 @@ else{
process get_valid_interaction_dnase{ process get_valid_interaction_dnase{
tag "$sample" tag "$sample"
publishDir "${params.outdir}/hic_results/data", mode: 'copy', publishDir "${params.outdir}/hic_results/data", mode: 'copy',
saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$filename" : "$filename"} saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$filename" : "$filename"}
input: input:
set val(sample), file(pe_bam) from paired_bam set val(sample), file(pe_bam) from paired_bam
output: output:
set val(sample), file("*.validPairs") into valid_pairs set val(sample), file("*.validPairs") into valid_pairs
set val(sample), file("*.validPairs") into valid_pairs_4cool set val(sample), file("*.validPairs") into valid_pairs_4cool
set val(sample), file("*RSstat") into all_rsstat set val(sample), file("*RSstat") into all_rsstat
script: script:
if (params.splitFastq){ if (params.splitFastq){
sample = sample.toString() - ~/(\.[0-9]+)$/ sample = sample.toString() - ~/(\.[0-9]+)$/
} }
...@@ -659,7 +650,7 @@ else{ ...@@ -659,7 +650,7 @@ else{
process remove_duplicates { process remove_duplicates {
tag "$sample" tag "$sample"
publishDir "${params.outdir}/hic_results/data", mode: 'copy', publishDir "${params.outdir}/hic_results/data", mode: 'copy',
saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$sample/$filename" : "$filename"} saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$sample/$filename" : "$filename"}
input: input:
set val(sample), file(vpairs) from valid_pairs.groupTuple() set val(sample), file(vpairs) from valid_pairs.groupTuple()
...@@ -674,7 +665,7 @@ process remove_duplicates { ...@@ -674,7 +665,7 @@ process remove_duplicates {
""" """
mkdir -p stats/${sample} mkdir -p stats/${sample}
sort -T /tmp/ -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \ sort -T /tmp/ -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat
cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
...@@ -764,7 +755,7 @@ process run_ice{ ...@@ -764,7 +755,7 @@ process run_ice{
--results_filename ${prefix}_iced.matrix \ --results_filename ${prefix}_iced.matrix \
--filter_high_counts_perc ${params.ice_filer_high_count_perc} \ --filter_high_counts_perc ${params.ice_filer_high_count_perc} \
--max_iter ${params.ice_max_iter} --eps ${params.ice_eps} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${rmaps} --max_iter ${params.ice_max_iter} --eps ${params.ice_eps} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${rmaps}
""" """
} }
...@@ -788,13 +779,13 @@ process generate_cool{ ...@@ -788,13 +779,13 @@ process generate_cool{
script: script:
""" """
hicpro2higlass.sh -i $vpairs -r 5000 -c ${chrsize} -n hicpro2higlass.sh -i $vpairs -r 5000 -c ${chrsize} -n
""" """
} }
/* /*
* STEP 5 - MultiQC * STEP 5 - MultiQC
*/ */
process multiqc { process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy' publishDir "${params.outdir}/MultiQC", mode: 'copy'
...@@ -814,23 +805,19 @@ process multiqc { ...@@ -814,23 +805,19 @@ process multiqc {
script: script:
rtitle = custom_runName ? "--title \"$custom_runName\"" : '' rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : '' rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
""" """
multiqc -f $rtitle $rfilename --config $multiqc_config . multiqc -f $rtitle $rfilename --config $multiqc_config .
""" """
} }
/****************************************************
* POST-PROCESSING
*/
/* /*
* Output Description HTML * STEP 3 - Output Description HTML
*/ */
process output_documentation { process output_documentation {
publishDir "${params.outdir}/Documentation", mode: 'copy' publishDir "${params.outdir}/pipeline_info", mode: 'copy'
input: input:
file output_docs from ch_output_docs file output_docs from ch_output_docs
...@@ -876,10 +863,26 @@ workflow.onComplete { ...@@ -876,10 +863,26 @@ workflow.onComplete {
if(workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository if(workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
if(workflow.container) email_fields['summary']['Docker image'] = workflow.container
email_fields['summary']['Nextflow Version'] = workflow.nextflow.version email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
email_fields['summary']['Nextflow Build'] = workflow.nextflow.build email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
// TODO nf-core: If not using MultiQC, strip out this code (including params.maxMultiqcEmailFileSize)
// On success try attach the multiqc report
def mqc_report = null
try {
if (workflow.success) {
mqc_report = multiqc_report.getVal()
if (mqc_report.getClass() == ArrayList){
log.warn "[nf-core/hic] Found multiple reports from process 'multiqc', will use only one"
mqc_report = mqc_report[0]
}
}
} catch (all) {
log.warn "[nf-core/hic] Could not attach MultiQC report to summary email"
}
// Render the TXT template // Render the TXT template
def engine = new groovy.text.GStringTemplateEngine() def engine = new groovy.text.GStringTemplateEngine()
def tf = new File("$baseDir/assets/email_template.txt") def tf = new File("$baseDir/assets/email_template.txt")
...@@ -892,7 +895,7 @@ workflow.onComplete { ...@@ -892,7 +895,7 @@ workflow.onComplete {
def email_html = html_template.toString() def email_html = html_template.toString()
// Render the sendmail template // Render the sendmail template
def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir" ] def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.maxMultiqcEmailFileSize.toBytes() ]
def sf = new File("$baseDir/assets/sendmail_template.txt") def sf = new File("$baseDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString() def sendmail_html = sendmail_template.toString()
...@@ -912,7 +915,7 @@ workflow.onComplete { ...@@ -912,7 +915,7 @@ workflow.onComplete {
} }
// Write summary e-mail HTML to a file // Write summary e-mail HTML to a file
def output_d = new File( "${params.outdir}/Documentation/" ) def output_d = new File( "${params.outdir}/pipeline_info/" )
if( !output_d.exists() ) { if( !output_d.exists() ) {
output_d.mkdirs() output_d.mkdirs()
} }
...@@ -921,5 +924,67 @@ workflow.onComplete { ...@@ -921,5 +924,67 @@ workflow.onComplete {
def output_tf = new File( output_d, "pipeline_report.txt" ) def output_tf = new File( output_d, "pipeline_report.txt" )
output_tf.withWriter { w -> w << email_txt } output_tf.withWriter { w -> w << email_txt }
log.info "[nf-core/hic] Pipeline Complete" c_reset = params.monochrome_logs ? '' : "\033[0m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_red = params.monochrome_logs ? '' : "\033[0;31m";
if (workflow.stats.ignoredCountFmt > 0 && workflow.success) {
log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCountFmt} ${c_reset}"
log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCountFmt} ${c_reset}"
}
if(workflow.success){
log.info "${c_purple}[nf-core/hic]${c_green} Pipeline completed successfully${c_reset}"
} else {
checkHostname()
log.info "${c_purple}[nf-core/hic]${c_red} Pipeline completed with errors${c_reset}"
}
}
def nfcoreHeader(){
// Log colors ANSI codes
c_reset = params.monochrome_logs ? '' : "\033[0m";
c_dim = params.monochrome_logs ? '' : "\033[2m";
c_black = params.monochrome_logs ? '' : "\033[0;30m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_yellow = params.monochrome_logs ? '' : "\033[0;33m";
c_blue = params.monochrome_logs ? '' : "\033[0;34m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_cyan = params.monochrome_logs ? '' : "\033[0;36m";
c_white = params.monochrome_logs ? '' : "\033[0;37m";
return """ ${c_dim}----------------------------------------------------${c_reset}
${c_green},--.${c_black}/${c_green},-.${c_reset}
${c_blue} ___ __ __ __ ___ ${c_green}/,-._.--~\'${c_reset}
${c_blue} |\\ | |__ __ / ` / \\ |__) |__ ${c_yellow}} {${c_reset}
${c_blue} | \\| | \\__, \\__/ | \\ |___ ${c_green}\\`-._,-`-,${c_reset}
${c_green}`._,._,\'${c_reset}
${c_purple} nf-core/hic v${workflow.manifest.version}${c_reset}
${c_dim}----------------------------------------------------${c_reset}
""".stripIndent()
}
def checkHostname(){
def c_reset = params.monochrome_logs ? '' : "\033[0m"
def c_white = params.monochrome_logs ? '' : "\033[0;37m"
def c_red = params.monochrome_logs ? '' : "\033[1;91m"
def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
if(params.hostnames){
def hostname = "hostname".execute().text.trim()
params.hostnames.each { prof, hnames ->
hnames.each { hname ->
if(hostname.contains(hname) && !workflow.profile.contains(prof)){
log.error "====================================================\n" +
" ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
" but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
" ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
"============================================================"
}
}
}
}
} }
nextflow.config
+ 19
− 10
View file @ 44b7a17b
...@@ -3,9 +3,6 @@ ...@@ -3,9 +3,6 @@
* nf-core/hic Nextflow config file * nf-core/hic Nextflow config file
* ------------------------------------------------- * -------------------------------------------------
* Default config options for all environments. * Default config options for all environments.
* Cluster-specific config options should be saved
* in the conf folder and imported under a profile
* name here.
*/ */
// Global default params, used in configs // Global default params, used in configs
...@@ -27,26 +24,38 @@ params { ...@@ -27,26 +24,38 @@ params {
// Boilerplate options // Boilerplate options
name = false name = false
multiqc_config = "$baseDir/conf/multiqc_config.yaml" multiqc_config = "$baseDir/assets/multiqc_config.yaml"
email = false email = false
maxMultiqcEmailFileSize = 25.MB
plaintext_email = false plaintext_email = false
monochrome_logs = false
help = false help = false
igenomes_base = "./iGenomes" igenomes_base = "./iGenomes"
tracedir = "${params.outdir}/pipeline_info" tracedir = "${params.outdir}/pipeline_info"
clusterOptions = false
awsqueue = false awsqueue = false
awsregion = 'eu-west-1' awsregion = 'eu-west-1'
igenomesIgnore = false igenomesIgnore = false
custom_config_version = 'master' custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_description = false
config_profile_contact = false
config_profile_url = false
} }
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'nfcore/hic:dev' process.container = 'nfcore/hic:dev'
// Load base.config by default for all pipelines // Load base.config by default for all pipelines
includeConfig 'conf/base.config' includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions // Load nf-core custom profiles from different Institutions
includeConfig "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/nfcore_custom.config" try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load hic config file // Load hic config file
includeConfig 'conf/hicpro.config' includeConfig 'conf/hicpro.config'
...@@ -71,19 +80,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] ...@@ -71,19 +80,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline { timeline {
enabled = true enabled = true
file = "${params.tracedir}/nf-core/hic_timeline.html" file = "${params.tracedir}/execution_timeline.html"
} }
report { report {
enabled = true enabled = true
file = "${params.tracedir}/nf-core/hic_report.html" file = "${params.tracedir}/execution_report.html"
} }
trace { trace {
enabled = true enabled = true
file = "${params.tracedir}/nf-core/hic_trace.txt" file = "${params.tracedir}/execution_trace.txt"
} }
dag { dag {
enabled = true enabled = true
file = "${params.tracedir}/nf-core/hic_dag.svg" file = "${params.tracedir}/pipeline_dag.svg"
} }
manifest { manifest {
......
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