nf-core¶
What is nf-core ?
¶
- a community
- a set of workflows
- a helper tools
Loading environment¶
On genobioinfo server, each time you want to use nf-core workflows, you will have to load one of the following module:
search_module nfcore
bioinfo/NextflowWorkflows/nfcore-Nextflow-v20.11.0-edge
bioinfo/NextflowWorkflows/nfcore-Nextflow-v21.10.6
bioinfo/NextflowWorkflows/nfcore-Nextflow-v22.12.0-edge
bioinfo/NextflowWorkflows/nfcore-Nextflow-v23.04.3
bioinfo/NextflowWorkflows/nfcore-Nextflow-v23.10.0
bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2
The nf-core module depends on the Nextflow module, you can choose the nextflow version you want to use.
module load bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2
Tips
To know what is contained in a module you can use the following command module show
module show bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2
-------------------------------------------------------------------
/tools/modulefiles/bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2:
module-whatis {loads the bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2 environment}
module load devel/java/17.0.6
module load containers/singularity/3.9.9
module load bioinfo/Nextflow/24.04.2
module load devel/python/Python-3.11.1
setenv NXF_SINGULARITY_CACHEDIR /usr/local/bioinfo/src/NextflowWorkflows/singularity-img/
-------------------------------------------------------------------
This will load :
- Nextflow module,
- singularity module,
- set the path to access to the local singularity images available in
/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/
List all available pipeline¶
By command line :¶
nf-core list
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nf-core/tools version 2.13 - https://nf-co.re
There is a new version of nf-core/tools available! (2.14.1)
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━┩
│ sarek │ 345 │ 3.4.2 │ 4 weeks ago │ - │ - │
│ funcscan │ 58 │ 1.1.5 │ 3 months ago │ - │ - │
│ scrnaseq │ 174 │ 2.6.0 │ 4 weeks ago │ - │ - │
│ crisprseq │ 22 │ 2.1.1 │ 6 months ago │ - │ - │
│ oncoanalyser │ 15 │ dev │ yesterday │ - │ - │
│ phaseimpute │ 15 │ dev │ yesterday │ - │ - │
│ raredisease │ 74 │ 2.1.0 │ 1 week ago │ - │ - │
│ proteinfold │ 41 │ 1.0.0 │ 1 years ago │ - │ - │
│ bacass │ 55 │ 2.2.0 │ 2 months ago │ - │ - │
│ bamtofastq │ 13 │ 2.1.1 │ 4 weeks ago │ - │ - │
│ airrflow │ 44 │ 4.1.0 │ 4 days ago │ - │ - │
│ reportho │ 4 │ dev │ 4 days ago │ - │ - │
│ rnavar │ 31 │ 1.0.0 │ 2 years ago │ 2 weeks ago │ No (master - 222d7a1) │
On https://nf-co.re/¶
Each pipeline has its own webpage at https://nf-co.re/PIPELINE.
See online documentation for rnaseq pipeline
In addition to this documentation, each pipeline comes with basic command line reference. This can be seen by running the pipeline with the --help flag, for example:
nextflow run nf-core/rnaseq --help
Note
Note that if you run nextflow run nf-core/rnaseq -help you will not have the same result !
Rnaseq workflow
Visit the page of the workflow rnaseq . Check which analyses are performed by default and what are the required parameters ?
Visit your favorite workflow
Visit the page of the workflow you are interrested in (https://nf-co.re). Explain :
- which analyses are performed ?
- which input format is expected ?
- which parameters are required ?
Fetching pipeline code¶
Unless you are actively developing pipeline code, we recommend using the Nextflow built-in functionality to fetch nf-core pipelines. Nextflow will automatically fetch the pipeline code when you run nextflow run nf-core/PIPELINE. For the best reproducibility, it is good to explicitly reference the pipeline version number that you wish to use with the -revision/-r flag. For example:
nextflow run nf-core/rnaseq -revision 3.14.0
If not specified, Nextflow will fetch the master branch - for nf-core pipelines this will be the latest release. If you would like to run the latest development code, use -r dev.
Note that once pulled, Nextflow will use the local cached version for subsequent runs. Use the -latest flag when running the pipeline to always fetch the latest version. Alternatively, you can force Nextflow to pull a pipeline again using the nextflow pull command:
nextflow pull nf-core/rnaseq
Tips
Get info on this pipeline with nextflow info command such as where is store the workflow code?
Test a workflow¶
Each workflow come with test data. The first thing to do, is to try your favorite workflow with option -profile test, as you are on genotoul you can add -profile test,genotoul. We will see later the content of those profiles. Make sure you are on a node srun --mem 4G --pty bash or create a script and run it with sbatch command.
$ nextflow run nf-core/rnaseq -profile test,genotoul --outdir results -r 3.14.0
Nextflow 24.04.1 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.0
Launching `https://github.com/nf-core/rnaseq` [lonely_feynman] DSL2 - revision: b89fac3265 [master]
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Multiple config files detected!
Please provide pipeline parameters via the CLI or Nextflow '-params-file' option.
Custom config files including those provided by the '-c' Nextflow option can be
used to provide any configuration except for parameters.
-profile test,genotoul --outdir results
Docs: https://nf-co.re/usage/configuration#custom-configuration-files
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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nf-core/rnaseq v3.14.0-gb89fac3
------------------------------------------------------
Core Nextflow options
revision : master
runName : lonely_feynman
containerEngine : singularity
launchDir : /work/user/bleuet/nextflow-tutorial
workDir : /work/user/bleuet/nextflow-tutorial/work
projectDir : /home/bleuet/.nextflow/assets/nf-core/rnaseq
userName : bleuet
profile : test
configFiles :
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv
outdir : results
Reference genome options
fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta
gtf : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz
gff : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz
transcript_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta
additional_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz
hisat2_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz
rsem_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz
salmon_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz
Read filtering options
bbsplit_fasta_list : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt
UMI options
umitools_bc_pattern : NNNN
Alignment options
pseudo_aligner : salmon
min_mapped_reads : 5
Optional outputs
save_reference : true
Process skipping options
skip_bbsplit : false
Institutional config options
config_profile_name : Test profile
config_profile_description: The Genotoul cluster profile
config_profile_contact : support.bioinfo.genotoul@inra.fr
config_profile_url : http://bioinfo.genotoul.fr/
Max job request options
max_cpus : 48
max_memory : 120 GB
max_time : 4d
...
...
...
[54/d45a5d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔
[20/af246c] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔
[a5/617edc] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO [100%] 1 of 1 ✔
[8a/748204] process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 ✔
[a0/93c353] process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1) [100%] 1 of 1 ✔
-[nf-core/rnaseq] Pipeline completed successfully -
Completed at: 27-May-2024 19:18:15
Duration : 6m 3s
CPU hours : 1.7
Succeeded : 194
Success
Thus you can see if the workflow run correctly on our infrastructure. This is a good news and the first thing to do before trying with you data.
Workflow version
Note that the first time you run a workflow you are not obliged to set the version with -r.
But as soon as your pipeline is installed locally, nextflow required it -r 3.14.0