Profiles

Profile genotoul

With the command nextflow run nf-core/rnaseq -profile genotoul, the profile genotoul.config will be automatically download and use.

This functionnality is only available with nf-core pipelines.

Multiple comma-separated config profiles can be specified in one go, so the following commands are perfectly valid:

nextflow run nf-core/rnaseq -profile test,singularity
nextflow run nf-core/hlatyping -profile debug,genotoul

Note that the order in which config profiles are specified matters. Their priority increases from left to right.

Profile test

The test profile is a bit of a special case. Whereas all other config profiles tell Nextflow how to run on different computational systems, the test profile configures each nf-core pipeline to run without any other command line flags. It specifies URLs for test data and all required parameters. Thanks to this, you can test any nf-core pipeline.

Test a pipeline with profile genotoul & test:

The first thing to do before executing a pipeline on your own data is to try with test profile.

$ nextflow run nf-core/rnaseq -r 3.0 -profile genotoul,test
N E X T F L O W  ~  version 20.11.0-edge
Launching `nf-core/rnaseq` [special_galileo] - revision: 3643a94411 [3.0]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v3.0
------------------------------------------------------

Core Nextflow options
    revision                  : 3.0
    runName                   : special_galileo
    containerEngine           : singularity
    launchDir                 : /work/cnoirot/nextflow_tutoriak
    workDir                   : /work/cnoirot/nextflow_tutoriak/work
    projectDir                : /home/cnoirot/.nextflow/assets/nf-core/rnaseq
    userName                  : cnoirot
    profile                   : genotoul,test
    configFiles               : /home/cnoirot/.nextflow/assets/nf-core/rnaseq/nextflow.config

Input/output options
    input                     : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/samplesheet.csv

UMI options
    umitools_bc_pattern       : NNNN

Reference genome options
    fasta                     : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa
    gtf                       : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz
    gff                       : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz
    transcript_fasta          : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta
    additional_fasta          : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz
    star_index                : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/star.tar.gz
    hisat2_index              : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz
    rsem_index                : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz
    salmon_index              : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz
    save_reference            : true
    igenomes_ignore           : true

Alignment options
    pseudo_aligner            : salmon

Institutional config options
    config_profile_description: Minimal test dataset to check pipeline function
    config_profile_contact    : support.bioinfo.genotoul@inra.fr
    config_profile_url        : http://bioinfo.genotoul.fr/

Max job request options
    max_cpus                  : 2
    max_memory                : 6 GB
    max_time                  : 2d

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Exercise 9:

• Remove the file nextflow.config in your current directory.

• Run the nf-core/rnaseq pipeline with profiles genotoul and test and follow the execution on cluster with squeue -u USERNAME in another terminal.

• List the options for rnaseq pipeline. Note that all options of all pipeline are detailled in each web page of each workflow.

• Copy directory /usr/local/bioinfo/src/NextflowWorkflows/example_on_cluster/data in current directory nextflow-tutorial

• Create a samplesheet with following lines samples.csv:

  group,replicate,fastq_1,fastq_2,strandedness
  mutant,1,data/MT_rep1_1_Ch6.fastq.gz,data/MT_rep1_2_Ch6.fastq.gz,unstranded
  wild,1,data/WT_rep1_1_Ch6.fastq.gz,data/WT_rep1_2_Ch6.fastq.gz,unstranded
  

• Run the pipeline with following data and parameters:

  • --fasta data/ITAG2.3_genomic_Ch6.fasta
  • --gtf data/ITAG2.3_genomic_Ch6.gtf
  • --input samples.csv
  • --outdir ResultsItag
  • aligner star & rsem
  • profile genotoul
  • revision 3.0

• Monitor job execution squeue -u USERNAME. On which queue the jobs are launched ?

• Copy ResultsItag directory into ~/public_html and visit http://genoweb.toulouse.inra.fr/~USERNAME/

• Does the memory was sufficient ? Which process is the longer ? (see execution_report.html)

• Visit the nf-core slack and check if a channel of the workflow you are interested in is open, check last discussions. What was the last discussion about?

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