nf-core
Link to section 'Description' of 'nf-core' Description
A community effort to collect a curated set of analysis pipelines built using Nextflow and tools to run the pipelines.
Home page: https://nf-co.re
Link to section 'Versions' of 'nf-core' Versions
- Anvil: 2.7.2, 2.8
- Negishi: 2.7.2, 2.8
Link to section 'Commands' of 'nf-core' Commands
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nf-core/tools version 2.8 - https://nf-co.re
Usage: nf-core [OPTIONS] COMMAND [ARGS]...
nf-core/tools provides a set of helper tools for use with nf-core Nextflow pipelines.
It is designed for both end-users running pipelines and also developers creating new pipelines.
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮
│ --version Show the version and exit. │
│ --verbose -v Print verbose output to the console. │
│ --hide-progress Don't show progress bars. │
│ --log-file -l Save a verbose log to a file. │
│ --help -h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands for users ─────────────────────────────────────────────────────────────────────────────╮
│ list List available nf-core pipelines with local info. │
│ launch Launch a pipeline using a web GUI or command line prompts. │
│ download Download a pipeline, nf-core/configs and pipeline singularity images. │
│ licences List software licences for a given workflow (DSL1 only). │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands for developers ────────────────────────────────────────────────────────────────────────╮
│ create Create a new pipeline using the nf-core template. │
│ lint Check pipeline code against nf-core guidelines. │
│ modules Commands to manage Nextflow DSL2 modules (tool wrappers). │
│ subworkflows Commands to manage Nextflow DSL2 subworkflows (tool wrappers). │
│ schema Suite of tools for developers to manage pipeline schema. │
│ bump-version Update nf-core pipeline version number. │
│ sync Sync a pipeline TEMPLATE branch with the nf-core template. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
Link to section 'Module' of 'nf-core' Module
You can load the modules by:
module load nf-core
Link to section 'List available pipelines' of 'nf-core' List available pipelines
To check all available pipelines:
$ nf-core list
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nf-core/tools version 2.8 - https://nf-co.re
┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃
┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━┩
│ funcscan │ 29 │ 1.1.0 │ 2 days ago │ - │ - │
│ smrnaseq │ 49 │ 2.2.0 │ 4 days ago │ - │ - │
│ rnafusion │ 95 │ 2.3.4 │ 4 days ago │ - │ - │
│ rnaseq │ 604 │ 3.11.2 │ 5 days ago │ 5 days ago │ No (dev - 4b7695a) │
│ demultiplex │ 26 │ 1.2.0 │ 5 days ago │ - │ - │
│ differentialabundan… │ 19 │ 1.2.0 │ 2 weeks ago │ 2 days ago │ Yes (v1.2.0) │
│ mhcquant │ 21 │ 2.4.1 │ 3 weeks ago │ - │ - │
│ viralintegration │ 8 │ 0.1.0 │ 1 months ago │ - │ - │
│ quantms │ 8 │ 1.1.1 │ 1 months ago │ - │ - │
│ viralrecon │ 93 │ 2.6.0 │ 1 months ago │ - │ - │
│ airrflow │ 24 │ 3.0 │ 1 months ago │ - │ - │
│ scrnaseq │ 81 │ 2.2.0 │ 1 months ago │ - │ - │
│ epitopeprediction │ 25 │ 2.2.1 │ 1 months ago │ - │ - │
│ isoseq │ 12 │ 1.1.4 │ 2 months ago │ - │ - │
│ taxprofiler │ 49 │ 1.0.0 │ 2 months ago │ 2 weeks ago │ No (master - c3f1adf) │
│ nanoseq │ 109 │ 3.1.0 │ 2 months ago │ - │ - │
│ cutandrun │ 41 │ 3.1 │ 2 months ago │ - │ - │
│ circdna │ 12 │ 1.0.2 │ 2 months ago │ - │ - │
│ ampliseq │ 111 │ 2.5.0 │ 2 months ago │ - │ - │
│ mag │ 126 │ 2.3.0 │ 2 months ago │ - │ - │
│ nascent │ 8 │ 2.1.1 │ 2 months ago │ - │ - │
│ phyloplace │ 3 │ 1.0.0 │ 2 months ago │ - │ - │
│ proteinfold │ 21 │ 1.0.0 │ 3 months ago │ - │ - │
│ crisprseq │ 8 │ 1.0 │ 3 months ago │ - │ - │
│ hic │ 48 │ 2.0.0 │ 3 months ago │ 2 weeks ago │ Yes (v2.0.0) │
│ sarek │ 235 │ 3.1.2 │ 4 months ago │ - │ - │
│ fetchngs │ 78 │ 1.9 │ 4 months ago │ - │ - │
│ methylseq │ 104 │ 2.3.0 │ 4 months ago │ - │ - │
│ atacseq │ 134 │ 2.0 │ 5 months ago │ - │ - │
│ eager │ 91 │ 2.4.6 │ 5 months ago │ 2 days ago │ Yes (v2.4.6) │
│ coproid │ 7 │ 1.1.1 │ 6 months ago │ - │ - │
│ hgtseq │ 16 │ 1.0.0 │ 6 months ago │ - │ - │
│ hlatyping │ 41 │ 2.0.0 │ 6 months ago │ - │ - │
│ chipseq │ 144 │ 2.0.0 │ 7 months ago │ - │ - │
│ rnavar │ 16 │ 1.0.0 │ 10 months ago │ - │ - │
│ mnaseseq │ 9 │ 1.0.0 │ 11 months ago │ - │ - │
│ hicar │ 3 │ 1.0.0 │ 12 months ago │ - │ - │
│ bamtofastq │ 8 │ 1.2.0 │ 1 years ago │ - │ - │
│ bacass │ 42 │ 2.0.0 │ 2 years ago │ 5 days ago │ Yes (v2.0.0) │
│ bactmap │ 41 │ 1.0.0 │ 2 years ago │ - │ - │
│ metaboigniter │ 10 │ 1.0.1 │ 2 years ago │ - │ - │
│ diaproteomics │ 10 │ 1.2.4 │ 2 years ago │ - │ - │
│ clipseq │ 13 │ 1.0.0 │ 2 years ago │ - │ - │
│ pgdb │ 3 │ 1.0.0 │ 2 years ago │ - │ - │
│ dualrnaseq │ 12 │ 1.0.0 │ 2 years ago │ - │ - │
│ cageseq │ 9 │ 1.0.2 │ 2 years ago │ - │ - │
│ proteomicslfq │ 29 │ 1.0.0 │ 3 years ago │ - │ - │
│ imcyto │ 20 │ 1.0.0 │ 3 years ago │ - │ - │
│ slamseq │ 4 │ 1.0.0 │ 3 years ago │ - │ - │
│ callingcards │ 1 │ dev │ - │ - │ - │
│ circrna │ 27 │ dev │ - │ - │ - │
│ fastquorum │ 8 │ dev │ - │ - │ - │
│ genomeannotator │ 9 │ dev │ - │ - │ - │
│ genomeassembler │ 12 │ dev │ - │ - │ - │
│ gwas │ 12 │ dev │ - │ - │ - │
│ lncpipe │ 25 │ dev │ - │ - │ - │
│ metapep │ 3 │ dev │ - │ - │ - │
│ metatdenovo │ 2 │ dev │ - │ - │ - │
│ nanostring │ 2 │ dev │ - │ - │ - │
│ pangenome │ 23 │ dev │ - │ 2 weeks ago │ No (a_brave_new_world │
│ │ │ │ │ │ - 6aa9b39) │
│ radseq │ 0 │ dev │ - │ - │ - │
│ raredisease │ 37 │ dev │ - │ - │ - │
│ rnadnavar │ 0 │ dev │ - │ - │ - │
│ rnasplice │ 3 │ dev │ - │ - │ - │
│ scflow │ 19 │ dev │ - │ - │ - │
│ spatialtranscriptom… │ 19 │ dev │ - │ - │ - │
│ spinningjenny │ 0 │ dev │ - │ - │ - │
│ variantcatalogue │ 3 │ dev │ - │ - │ - │
└──────────────────────┴───────┴────────────────┴───────────────┴─────────────┴───────────────────────┘
Link to section 'Download pipelines' of 'nf-core' Download pipelines
It is highly recommended to download pipelines to clusters before running them. Using singularity containers to run these pipelines are also recommended. Befor downloading, please set up environment variables NXF_SINGULARITY_CACHEDIR for singularity cache or NXF_CONDA_CACHEDIR for conda cache. Below is an example you can add to .bashrc for bash users.
export NXF_SINGULARITY_CACHEDIR="$SCRATCH/singularity/cache"
export NXF_CONDA_CACHEDIR="$SCRATCH/conda/cache"
Below is the example to download the rnaseq pipeline:
$ nf-core download rnaseq
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nf-core/tools version 2.8 - https://nf-co.re
? Select release / branch: (Use arrow keys)
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Link to section 'Run the pipeline' of 'nf-core' Run the pipeline
If users have downloaded the rnaseq pipeline to a folder called nf-core under $HOME, users can use it to run RNAseq analysis. Here is an example for running RNAseq analysis with human samples.
#!/bin/bash
#SBATCH -A XXXX
#SBATCH --job-name=rnaseq
#SBATCH --output=slurm-%A.%a.out
#SBATCH --error=slurm-%A.%a.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=64
#SBATCH --time=24:00:00
#SBATCH --mail-type=all
module load nextflow
nextflow run $HOME/nf-core/nf-core-rnaseq-3.11.2/workflow/ \
--input samplesheet.csv --outdir results \
--genome GRCh37 -profile singularity