Using singularity with Nextflow

To use singularity on genotoul, you have to define by a config file the required options.

While using singularity with Nextflow, you don't have access to all the mounted directory, such as /work or /save. To work around this problem use runOptions and -B to define bind paths.

To activate usage of singularity with nextflow you can use

• option -with-singularity in command line or
• write in nextflow.config following lines:

  singularity {
  enabled = true
  autoMount = true
  runOptions = '-B /bank -B /work2 -B /work -B /save -B /home'
  }
  

Run a workflow from a repository with dependancies

The workflow nextflow-io/rnaseq have bowtie2 as dependancies. Try to run it whitout activating singularity :

$ nextflow run nextflow-io/rnaseq -r v1.5

N E X T F L O W  ~  version 20.10.0
Launching `nextflow-io/rnaseq` [nasty_chandrasekhar] - revision: b5af40f295 [v1.5]
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [329c1992a6]
R N A T O Y   P I P E L I N E    
=============================
genome: /home/cnoirot/.nextflow/assets/nextflow-io/rnaseq/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
annot : /home/cnoirot/.nextflow/assets/nextflow-io/rnaseq/data/ggal/ggal_1_48850000_49020000.bed.gff
reads : /home/cnoirot/.nextflow/assets/nextflow-io/rnaseq/data/ggal/*_{1,2}.fq
outdir: results
executor >  local (1)
executor >  local (1)
[ce/62dab6] process > buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank) [100%] 1 of 1, failed: 1 ✘
[-        ] process > mapping                                                 -
[-        ] process > makeTranscript                                          -
Error executing process > 'buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank)'

Caused by:
  Process `buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank)` terminated with an error exit status (127)

Command executed:

  bowtie2-build --threads 1 ggal_1_48850000_49020000.Ggal71.500bpflank.fa genome.index

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: ligne2: bowtie2-build : commande introuvable

Work dir:
  /work/cnoirot/nextflow_tutoriak/work/ce/62dab6fc956aaa872b1af4690e261a

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Get an error ? Dependencies are not present !

To work around this error,

• load singularity module

  module load system/singularity-3.0.1
  

• and copy those lines into nextflow.config

  singularity {
  enabled = true
  autoMount = true
  runOptions = '-B /bank -B /work2 -B /work -B /save -B /home'
  }
  

• Then rerun the command

module load system/singularity-3.0.1
$ nextflow run nextflow-io/rnaseq -r v1.5 
N E X T F L O W  ~  version 20.10.0
Launching `nextflow-io/rnaseq` [jolly_monod] - revision: b5af40f295 [v1.5]
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [329c1992a6]
R N A T O Y   P I P E L I N E    
=============================
genome: /home/cnoirot/.nextflow/assets/nextflow-io/rnaseq/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
annot : /home/cnoirot/.nextflow/assets/nextflow-io/rnaseq/data/ggal/ggal_1_48850000_49020000.bed.gff
reads : /home/cnoirot/.nextflow/assets/nextflow-io/rnaseq/data/ggal/*_{1,2}.fq
outdir: results
executor >  local (5)
executor >  local (5)
[6c/0c7376] process > buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank) [100%] 1 of 1 ✔
[f6/0e3bb4] process > mapping (ggal_liver)                                    [100%] 2 of 2 ✔
[65/8cc4c3] process > makeTranscript (ggal_gut)                               [100%] 2 of 2 ✔

This configuration activate usage of a singularity image.

Exercise 7 :

Execute all steps describe in this page.