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HELP.nf
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/*
=========================================================================================
NANOME(Nanopore methylation) pipeline for Oxford Nanopore sequencing
=========================================================================================
NANOME Analysis Pipeline.
#### Homepage / Documentation
https://github.com/LabShengLi/nanome
@Author : Yang Liu
@FileName : HELP.nf
@Software : NANOME project
@Organization : JAX Sheng Li Lab
----------------------------------------------------------------------------------------
*/
def helpMessage() {
log.info"""
NANOME - Nextflow PIPELINE (v$workflow.manifest.version)
by Sheng Li Lab at The Jackson Laboratory
https://github.com/LabShengLi/nanome
=================================
Usage:
The typical command is as follows:
nextflow run LabShengLi/nanome -profile test,docker
nextflow run LabShengLi/nanome -profile test,singularity
nextflow run LabShengLi/nanome -profile [docker/singularity] \\
--dsname DSNAME --input INPUT --genome GENOME
Mandatory arguments:
--dsname Dataset/analysis name
--input Input path for raw fast5 files (folders, tar/tar.gz files)
--genome Genome reference name ('hg38', 'ecoli', or 'hg38_chr22') or a directory, the directory must contain only one .fasta file with .fasta.fai index file. Default is hg38
General options:
--processors Processors used for each task
--outdir Output dir, default is 'results'
--chrSet Chromosomes used in analysis, default is chr1-22, X and Y, for human. For E. coli data, it is default as 'NC_000913.3'. For other reference genome, please specify each chromosome with space seperated.
--cleanAnalyses If clean old basecalling info in fast5 files
--skipBasecall Skip redo basecalling if users provide basecalled inputs
--cleanup If clean work dir after complete, default is false
Tools specific options:
--run[Tool-name] By default, we run top four performers in nanome paper, specify '--run[Tool-name]' can include other tool, supported tools: NANOME, Megalodon, Nanopolish, DeepSignal, Guppy, Tombo, METEORE, and DeepMod
--rerioDir Rerio dir for Megalodon model, default will get online
--MEGALODON_MODEL Megalodon model name, default is 'res_dna_r941_min_modbases_5mC_v001.cfg'
--guppyDir Guppy installation local directory, used only for conda environment
--GUPPY_BASECALL_MODEL Guppy basecalling model, default is 'dna_r9.4.1_450bps_hac.cfg'
--GUPPY_METHCALL_MODEL Guppy methylation calling model, default is 'dna_r9.4.1_450bps_modbases_5mc_hac.cfg'
--deepsignalDir DeepSignal model dir, default will get online
--tomboResquiggleOptions Tombo resquiggle options for super long/damaged sequencing, set to '--signal-length-range 0 500000 --sequence-length-range 0 50000'
--moveOption If using move table for DeepMod, default is true
--useDeepModCluster If using DeepMod cluster model for human, default is false
--METEOREDir METEORE model dir, default will get online
Running environment options:
--docker_name Docker name used for pipeline, default is 'liuyangzzu/nanome:latest'
--singularity_name Singularity name used for pipeline, default is 'docker://liuyangzzu/nanome:latest'
--singularity_cache Singularity cache dir, default is 'local_singularity_cache'
--conda_name Conda name used for pipeline, default is 'nanome'
--conda_base_dir Conda base directory, default is '/opt/conda'
Platform specific options:
--queue SLURM job submission queue name, e.g., 'gpu'
--qos SLURM job submission QOS name, e.g., 'inference'
--gresOptions SLURM job submission GPU allocation option, e.g., 'gpu:v100:1'
--time SLURM job submission running time, e.g., '2h', '1d'
--memory SLURM job submission memory, e.g., '32GB'
--projectCloud Google Cloud Platform (GCP) project name for google-lifesciences
--config Lifebit CloudOS config file, e.g., 'conf/executors/lifebit.config'
-profile options:
Use this parameter to choose a predefined configuration profile. Profiles can give configuration presets for different compute environments.
test A bundle of input params for ecoli test
test_human A bundle of input params for human test
docker A generic configuration profile to be used with Docker, pulls software from Docker Hub: liuyangzzu/nanome:latest
singularity A generic configuration profile to be used with Singularity, pulls software from: docker://liuyangzzu/nanome:latest
conda Please only use conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity. Check our GitHub for how to install local conda environment
hpc A generic configuration profile to be used on HPC cluster with SLURM
google A generic configuration profile to be used on Google Cloud platform with 'google-lifesciences'
Contact to https://github.com/LabShengLi/nanome/issues for bug report.
""".stripIndent()
}