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# nf-core/hic: Troubleshooting
<!-- TODO nf-core: Change this documentation if these parameters/errors are not relevant for your workflow -->
## Input files not found
If only no file, only one input file , or only read one and not read two is picked up then something is wrong with your input file declaration
1. The path must be enclosed in quotes (`'` or `"`)
2. The path must have at least one `*` wildcard character. This is even if you are only running one paired end sample.
3. When using the pipeline with paired end data, the path must use `{1,2}` or `{R1,R2}` notation to specify read pairs.
4. If you are running Single end data make sure to specify `--singleEnd`
If the pipeline can't find your files then you will get the following error
```
ERROR ~ Cannot find any reads matching: *{1,2}.fastq.gz
```
Note that if your sample name is "messy" then you have to be very particular with your glob specification. A file name like `L1-1-D-2h_S1_L002_R1_001.fastq.gz` can be difficult enough for a human to read. Specifying `*{1,2}*.gz` wont work give you what you want Whilst `*{R1,R2}*.gz` will.
## Data organization
The pipeline can't take a list of multiple input files - it takes a glob expression. If your input files are scattered in different paths then we recommend that you generate a directory with symlinked files. If running in paired end mode please make sure that your files are sensibly named so that they can be properly paired. See the previous point.
## Extra resources and getting help
If you still have an issue with running the pipeline then feel free to contact us.
Have a look at the [pipeline website](https://github.com/nf-core/hic) to find out how.
If you have problems that are related to Nextflow and not our pipeline then check out the [Nextflow gitter channel](https://gitter.im/nextflow-io/nextflow) or the [google group](https://groups.google.com/forum/#!forum/nextflow).
docs/usage.md
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# nf-core/hic: Usage
## Table of contents
* [Introduction](#general-nextflow-info)
* [Running the pipeline](#running-the-pipeline)
* [Updating the pipeline](#updating-the-pipeline)
* [Reproducibility](#reproducibility)
* [Main arguments](#main-arguments)
* [`-profile`](#-profile-single-dash)
* [`awsbatch`](#awsbatch)
* [`conda`](#conda)
* [`docker`](#docker)
* [`singularity`](#singularity)
* [`test`](#test)
* [`--reads`](#--reads)
* [`--singleEnd`](#--singleend)
* [Reference genomes](#reference-genomes)
* [`--genome`](#--genome)
* [`--fasta`](#--fasta)
* [`--igenomesIgnore`](#--igenomesignore)
* [Job resources](#job-resources)
* [Automatic resubmission](#automatic-resubmission)
* [Custom resource requests](#custom-resource-requests)
* [AWS batch specific parameters](#aws-batch-specific-parameters)
* [`-awsbatch`](#-awsbatch)
* [`--awsqueue`](#--awsqueue)
* [`--awsregion`](#--awsregion)
* [Other command line parameters](#other-command-line-parameters)
* [`--outdir`](#--outdir)
* [`--email`](#--email)
* [`-name`](#-name-single-dash)
* [`-resume`](#-resume-single-dash)
* [`-c`](#-c-single-dash)
* [`--custom_config_version`](#--custom_config_version)
* [`--max_memory`](#--max_memory)
* [`--max_time`](#--max_time)
* [`--max_cpus`](#--max_cpus)
* [`--plaintext_email`](#--plaintext_email)
* [`--multiqc_config`](#--multiqc_config)
## General Nextflow info
Nextflow handles job submissions on SLURM or other environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through `screen` / `tmux` or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.
It is recommended to limit the Nextflow Java virtual machines memory. We recommend adding the following line to your environment (typically in `~/.bashrc` or `~./bash_profile`):
## Introduction
<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
```bash
NXF_OPTS='-Xms1g -Xmx4g'
```
<!-- TODO nf-core: Document required command line parameters to run the pipeline-->
## Running the pipeline
The typical command for running the pipeline is as follows:
```bash
nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile docker
nextflow run nf-core/hic --input '*_R{1,2}.fastq.gz' -profile docker
```
This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
......@@ -67,6 +24,7 @@ results # Finished results (configurable, see below)
```
### Updating the pipeline
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:
```bash
......@@ -74,181 +32,90 @@ nextflow pull nf-core/hic
```
### Reproducibility
It's 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.
## Core Nextflow arguments
## Main arguments
> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
### `-profile`
Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. Note that multiple profiles can be loaded, for example: `-profile docker` - the order of arguments is important!
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`
* A generic configuration profile to be used with AWS Batch.
* `conda`
* A generic configuration profile to be used with [conda](https://conda.io/docs/)
* Pulls most software from [Bioconda](https://bioconda.github.io/)
* `docker`
* 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/)
* `singularity`
* A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/)
* Pulls software from singularity-hub
* `test`
* A profile with a complete configuration for automated testing
* Includes links to test data so needs no other parameters
<!-- TODO nf-core: Document required command line parameters -->
### `--reads`
Use this to specify the location of your input FastQ files. For example:
Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
```bash
--reads 'path/to/data/sample_*_{1,2}.fastq'
```
Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Conda) - see below.
Please note the following requirements:
> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
1. The path must be enclosed in quotes
2. The path must have at least one `*` wildcard character
3. When using the pipeline with paired end data, the path must use `{1,2}` notation to specify read pairs.
The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
They are loaded in sequence, so later profiles can overwrite earlier profiles.
### `--singleEnd`
By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--singleEnd` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
```bash
--singleEnd --reads '*.fastq'
```
It is not possible to run a mixture of single-end and paired-end files in one run.
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.
* `docker`
* A generic configuration profile to be used with [Docker](https://docker.com/)
* Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
* `singularity`
* A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
* Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
* `conda`
* Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker or Singularity.
* A generic configuration profile to be used with [Conda](https://conda.io/docs/)
* Pulls most software from [Bioconda](https://bioconda.github.io/)
* `test`
* A profile with a complete configuration for automated testing
* Includes links to test data so needs no other parameters
## Reference genomes
### `-resume`
The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.
Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.
### `--genome` (using iGenomes)
There are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.
You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
You can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:
### `-c`
* Human
* `--genome GRCh37`
* Mouse
* `--genome GRCm38`
* _Drosophila_
* `--genome BDGP6`
* _S. cerevisiae_
* `--genome 'R64-1-1'`
Specify the path to a specific config file (this is a core NextFlow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
> There are numerous others - check the config file for more.
#### Custom resource requests
Note that you can use the same configuration setup to save sets of reference files for your own use, even if they are not part of the iGenomes resource. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for instructions on where to save such a file.
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.
The syntax for this reference configuration is as follows:
Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `star` 32GB of memory, you could use the following config:
<!-- TODO nf-core: Update reference genome example according to what is needed -->
```nextflow
params {
genomes {
'GRCh37' {
fasta = '<path to the genome fasta file>' // Used if no star index given
}
// Any number of additional genomes, key is used with --genome
process {
withName: star {
memory = 32.GB
}
}
```
<!-- TODO nf-core: Describe reference path flags -->
### `--fasta`
If you prefer, you can specify the full path to your reference genome when you run the pipeline:
```bash
--fasta '[path to Fasta reference]'
```
### `--igenomesIgnore`
Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
## Job resources
### 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.
### Custom resource requests
Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files hosted at [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information.
If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
If you have any questions or issues please send us a message on [`Slack`](https://nf-core-invite.herokuapp.com/).
## AWS Batch specific parameters
Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration. Please use the `-awsbatch` profile and then specify all of the following parameters.
### `--awsqueue`
The JobQueue that you intend to use on AWS Batch.
### `--awsregion`
The AWS region to run your job in. Default is set to `eu-west-1` but can be adjusted to your needs.
Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a S3 storage bucket of your choice - you'll get an error message notifying you if you didn't.
## Other command line parameters
<!-- TODO nf-core: Describe any other command line flags here -->
### `--outdir`
The output directory where the results will be saved.
### `--email`
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to speicfy this on the command line for every run.
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).
### `-name`
Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
### Running in the background
This is used in the MultiQC report (if not default) and in the summary HTML / e-mail (always).
Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
**NB:** Single hyphen (core Nextflow option)
The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file.
### `-resume`
Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.
You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
**NB:** Single hyphen (core Nextflow option)
### `-c`
Specify the path to a specific config file (this is a core NextFlow command).
Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time.
Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs).
**NB:** Single hyphen (core Nextflow option)
#### Nextflow memory requirements
Note - you can use this to override pipeline defaults.
### `--custom_config_version`
Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.
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`):
```bash
## Download and use config file with following git commid id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
NXF_OPTS='-Xms1g -Xmx4g'
```
### `--max_memory`
Use to set a top-limit for the default memory requirement for each process.
Should be a string in the format integer-unit. eg. `--max_memory '8.GB'`
### `--max_time`
Use to set a top-limit for the default time requirement for each process.
Should be a string in the format integer-unit. eg. `--max_time '2.h'`
### `--max_cpus`
Use to set a top-limit for the default CPU requirement for each process.
Should be a string in the format integer-unit. eg. `--max_cpus 1`
### `--plaintext_email`
Set to receive plain-text e-mails instead of HTML formatted.
### `--multiqc_config`
Specify a path to a custom MultiQC configuration file.
environment.yml
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name: nf-core-hic-1.0dev
# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-hic-1.2.1
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- conda-forge::python=3.7.3
- conda-forge::markdown=3.1.1
- conda-forge::pymdown-extensions=6.0
- conda-forge::pygments=2.5.2
# TODO nf-core: Add required software dependencies here
- fastqc=0.11.8
- multiqc=1.6
- bioconda::fastqc=0.11.8
- bioconda::multiqc=1.7
main.nf
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nextflow.config
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......@@ -3,83 +3,107 @@
* nf-core/hic Nextflow config file
* -------------------------------------------------
* 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
params {
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :latest
container = 'nfcore/hic:latest'
// Workflow flags
// TODO nf-core: Specify your pipeline's command line flags
reads = "data/*{1,2}.fastq.gz"
singleEnd = false
genome = false
input = "data/*{1,2}.fastq.gz"
single_end = false
outdir = './results'
publish_dir_mode = 'copy'
// Boilerplate options
name = false
multiqc_config = "$baseDir/conf/multiqc_config.yaml"
multiqc_config = false
email = false
email_on_fail = false
max_multiqc_email_size = 25.MB
plaintext_email = false
monochrome_logs = false
help = false
igenomes_base = "./iGenomes"
igenomes_base = 's3://ngi-igenomes/igenomes/'
tracedir = "${params.outdir}/pipeline_info"
clusterOptions = false
awsqueue = false
awsregion = 'eu-west-1'
igenomesIgnore = false
igenomes_ignore = false
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_description = false
config_profile_contact = false
config_profile_url = false
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 16
max_time = 240.h
}
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'nfcore/hic:dev'
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
includeConfig "https://raw.githubusercontent.com/nf-core/configs/${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: ${params.custom_config_base}/nfcore_custom.config")
}
profiles {
awsbatch { includeConfig 'conf/awsbatch.config' }
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
process.container = params.container
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
// once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
singularity.autoMounts = true
}
test { includeConfig 'conf/test.config' }
}
// Load igenomes.config if required
if(!params.igenomesIgnore){
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/nf-core/hic_timeline.html"
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/nf-core/hic_report.html"
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/nf-core/hic_trace.txt"
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/nf-core/hic_dag.svg"
file = "${params.tracedir}/pipeline_dag.svg"
}
manifest {
......@@ -88,16 +112,16 @@ manifest {
homePage = 'https://github.com/nf-core/hic'
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
mainScript = 'main.nf'
nextflowVersion = '>=0.32.0'
version = '1.0dev'
nextflowVersion = '>=19.10.0'
version = '1.2.1'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if(type == 'memory'){
if (type == 'memory') {
try {
if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
......@@ -105,9 +129,9 @@ def check_max(obj, type) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'time'){
} else if (type == 'time') {
try {
if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
......@@ -115,7 +139,7 @@ def check_max(obj, type) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'cpus'){
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
......
nextflow_schema.json 0 → 100644
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{
"$schema": "https://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/hic/master/nextflow_schema.json",
"title": "nf-core/hic pipeline parameters",
"description": "Analysis of Chromosome Conformation Capture data (Hi-C)",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"input"
],
"properties": {
"input": {
"type": "string",
"fa_icon": "fas fa-dna",
"description": "Input FastQ files.",
"help_text": "Use this to specify the location of your input FastQ files. For example:\n\n```bash\n--input 'path/to/data/sample_*_{1,2}.fastq'\n```\n\nPlease note the following requirements:\n\n1. The path must be enclosed in quotes\n2. The path must have at least one `*` wildcard character\n3. When using the pipeline with paired end data, the path must use `{1,2}` notation to specify read pairs.\n\nIf left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`"
},
"single_end": {
"type": "boolean",
"description": "Specifies that the input is single-end reads.",
"fa_icon": "fas fa-align-center",
"help_text": "By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--single_end` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--input`. For example:\n\n```bash\n--single_end --input '*.fastq'\n```\n\nIt is not possible to run a mixture of single-end and paired-end files in one run."
},
"outdir": {
"type": "string",
"description": "The output directory where the results will be saved.",
"default": "./results",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
}
}
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Options for the reference genome indices used to align reads.",
"properties": {
"genome": {
"type": "string",
"description": "Name of iGenomes reference.",
"fa_icon": "fas fa-book",
"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`.\n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
},
"fasta": {
"type": "string",
"fa_icon": "fas fa-font",
"description": "Path to FASTA genome file.",
"help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
},
"igenomes_base": {
"type": "string",
"description": "Directory / URL base for iGenomes references.",
"default": "s3://ngi-igenomes/igenomes/",
"fa_icon": "fas fa-cloud-download-alt",
"hidden": true
},
"igenomes_ignore": {
"type": "boolean",
"description": "Do not load the iGenomes reference config.",
"fa_icon": "fas fa-ban",
"hidden": true,
"help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
"description": "Display help text.",
"hidden": true,
"fa_icon": "fas fa-question-circle"
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"hidden": true,
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"mov"
]
},
"name": {
"type": "string",
"description": "Workflow name.",
"fa_icon": "fas fa-fingerprint",
"hidden": true,
"help_text": "A custom name for the pipeline run. Unlike the core nextflow `-name` option with one hyphen this parameter can be reused multiple times, for example if using `-resume`. Passed through to steps such as MultiQC and used for things like report filenames and titles."
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"hidden": true,
"help_text": "This works exactly as with `--email`, except emails are only sent if the workflow is not successful."
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true,
"help_text": "Set to receive plain-text e-mails instead of HTML formatted."
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true,
"help_text": "If file generated by pipeline exceeds the threshold, it will not be attached."
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true,
"help_text": "Set to disable colourful command line output and live life in monochrome."
},
"multiqc_config": {
"type": "string",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${params.outdir}/pipeline_info",
"fa_icon": "fas fa-cogs",
"hidden": true
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"default": 16,
"fa_icon": "fas fa-microchip",
"hidden": true,
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"default": "128.GB",
"fa_icon": "fas fa-memory",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog",
"help_text": "Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default: `master`.\n\n```bash\n## Download and use config file with following git commit id\n--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96\n```"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the `custom_config_base` option. For example:\n\n```bash\n## Download and unzip the config files\ncd /path/to/my/configs\nwget https://github.com/nf-core/configs/archive/master.zip\nunzip master.zip\n\n## Run the pipeline\ncd /path/to/my/data\nnextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/\n```\n\n> Note that the nf-core/tools helper package has a `download` command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.",
"fa_icon": "fas fa-users-cog"
},
"hostnames": {
"type": "string",
"description": "Institutional configs hostname.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/institutional_config_options"
}
]
}
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