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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| /* | ||
| ========================================================================================= | ||
| NANOME(Nanopore methylation) pipeline for Oxford Nanopore sequencing | ||
| ========================================================================================= | ||
| NANOME Analysis Pipeline. | ||
| #### Homepage / Documentation | ||
| https://github.com/LabShengLi/nanome | ||
| @Author : Yang Liu | ||
| @FileName : COMMONS.nf | ||
| @Software : NANOME project | ||
| @Organization : JAX Sheng Li Lab | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
| // check nextflow version, then declare DSL2 in two ways | ||
| def nextflowVersionCheck() { | ||
| // We now support both latest and lower versions, due to Lifebit CloudOS is only support 20.04 | ||
| // Note: NXF_VER=20.04.1 nextflow run main.nf -profile test,singularity | ||
| if( nextflow.version.matches(">= 20.07.1") ){ | ||
| nextflow.enable.dsl = 2 | ||
| } else { | ||
| // Support lower version of nextflow | ||
| nextflow.preview.dsl = 2 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| /* | ||
| ========================================================================================= | ||
| 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() | ||
| } | ||
|
|
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