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Autodetect max number of cores and pass as an argument in Nextflow

What is the difference between a Bioinformatics pipeline and workflow?

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3

$begingroup$

I am creating a pipeline in Nextflow. One step is creating a pangenome with Roary. Roary takes threads as an argument and if no number of threads is supplied as an argument it defaults to one.

Is there a way in Nextflow to pass the maximum number of available threads as an argument? At the moment the best I can come up with is defining an arbitrarily large number of threads as an argument which will cap out and run with the max number of threads. I would like to know, is there a 'cleaner' or more canonical way of doing this?

At the moment my process looks like this:

process roary 

 publishDir "$params.outdir/roary", mode: 'copy'

 cpus 200

 input:
 file gff from gff.collect()

 output:
 file("*") into roary
 file("pan_genome_reference.fa") into pan_genome
 file("pan_genome_sequences/*") into alignment_files
 file("gene_presence_absence.Rtab") into gene_presence
 set file("*accessory*"),
 file("*.Rtab"),
 file("_*"),
 file("*.txt"),
 file("*csv") into roary_out


 script:
 """
 roary -p $task.cpus -e -n -v -z $gff
 """

Thanks in advance. Also, apologies as I can see why this might not strictly be bioinformatics, but it's where Nextflow has the most traction.

workflow-management roary nextflow pangenome

share|improve this question

edited May 29 at 13:06

Daniel Standage

3,48777 silver badges3333 bronze badges

asked May 29 at 10:55

TW93TW93

17988 bronze badges

$endgroup$

• 
  
  
  

  
  2
  

  
  
  
  
  
  

  
  $begingroup$
  Workflow management has a firm foothold in bioinformatics and is in my opinion directly on topic on this site.
  $endgroup$
  – Daniel Standage
  May 29 at 13:01
  

  
  
  
  

add a comment
 | 

3

$begingroup$

I am creating a pipeline in Nextflow. One step is creating a pangenome with Roary. Roary takes threads as an argument and if no number of threads is supplied as an argument it defaults to one.

Is there a way in Nextflow to pass the maximum number of available threads as an argument? At the moment the best I can come up with is defining an arbitrarily large number of threads as an argument which will cap out and run with the max number of threads. I would like to know, is there a 'cleaner' or more canonical way of doing this?

At the moment my process looks like this:

process roary 

 publishDir "$params.outdir/roary", mode: 'copy'

 cpus 200

 input:
 file gff from gff.collect()

 output:
 file("*") into roary
 file("pan_genome_reference.fa") into pan_genome
 file("pan_genome_sequences/*") into alignment_files
 file("gene_presence_absence.Rtab") into gene_presence
 set file("*accessory*"),
 file("*.Rtab"),
 file("_*"),
 file("*.txt"),
 file("*csv") into roary_out


 script:
 """
 roary -p $task.cpus -e -n -v -z $gff
 """

Thanks in advance. Also, apologies as I can see why this might not strictly be bioinformatics, but it's where Nextflow has the most traction.

workflow-management roary nextflow pangenome

share|improve this question

edited May 29 at 13:06

Daniel Standage

3,48777 silver badges3333 bronze badges

asked May 29 at 10:55

TW93TW93

17988 bronze badges

$endgroup$

• 
  
  
  

  
  2
  

  
  
  
  
  
  

  
  $begingroup$
  Workflow management has a firm foothold in bioinformatics and is in my opinion directly on topic on this site.
  $endgroup$
  – Daniel Standage
  May 29 at 13:01
  

  
  
  
  

add a comment
 | 

$begingroup$

I am creating a pipeline in Nextflow. One step is creating a pangenome with Roary. Roary takes threads as an argument and if no number of threads is supplied as an argument it defaults to one.

Is there a way in Nextflow to pass the maximum number of available threads as an argument? At the moment the best I can come up with is defining an arbitrarily large number of threads as an argument which will cap out and run with the max number of threads. I would like to know, is there a 'cleaner' or more canonical way of doing this?

At the moment my process looks like this:

process roary 

 publishDir "$params.outdir/roary", mode: 'copy'

 cpus 200

 input:
 file gff from gff.collect()

 output:
 file("*") into roary
 file("pan_genome_reference.fa") into pan_genome
 file("pan_genome_sequences/*") into alignment_files
 file("gene_presence_absence.Rtab") into gene_presence
 set file("*accessory*"),
 file("*.Rtab"),
 file("_*"),
 file("*.txt"),
 file("*csv") into roary_out


 script:
 """
 roary -p $task.cpus -e -n -v -z $gff
 """

Thanks in advance. Also, apologies as I can see why this might not strictly be bioinformatics, but it's where Nextflow has the most traction.

workflow-management roary nextflow pangenome

share|improve this question

edited May 29 at 13:06

Daniel Standage

3,48777 silver badges3333 bronze badges

asked May 29 at 10:55

TW93TW93

17988 bronze badges

$endgroup$

process roary 

 publishDir "$params.outdir/roary", mode: 'copy'

 cpus 200

 input:
 file gff from gff.collect()

 output:
 file("*") into roary
 file("pan_genome_reference.fa") into pan_genome
 file("pan_genome_sequences/*") into alignment_files
 file("gene_presence_absence.Rtab") into gene_presence
 set file("*accessory*"),
 file("*.Rtab"),
 file("_*"),
 file("*.txt"),
 file("*csv") into roary_out


 script:
 """
 roary -p $task.cpus -e -n -v -z $gff
 """

share|improve this question

edited May 29 at 13:06

Daniel Standage

3,48777 silver badges3333 bronze badges

asked May 29 at 10:55

TW93TW93

17988 bronze badges

share|improve this question

edited May 29 at 13:06

Daniel Standage

3,48777 silver badges3333 bronze badges

asked May 29 at 10:55

TW93TW93

17988 bronze badges

edited May 29 at 13:06

Daniel Standage

3,48777 silver badges3333 bronze badges

edited May 29 at 13:06

Daniel Standage

3,48777 silver badges3333 bronze badges

asked May 29 at 10:55

TW93TW93

17988 bronze badges

asked May 29 at 10:55

TW93TW93

17988 bronze badges

1 Answer
1

active

oldest

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4

$begingroup$

I have not read the full Nextflow manual in depth, but I think there is no Nextflow command to detect the maximum number of threads you can use.

However, you can try to automatize this task by using the nproc command.

nproc gives you the number of processing units available. An idea would be to include something such nproc - 1 as the max number of threads for Roary.

share|improve this answer

edited May 29 at 13:57

terdon♦

5,82522 gold badges99 silver badges3333 bronze badges

answered May 29 at 12:20

platplat

74722 silver badges1212 bronze badges

$endgroup$

• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  Thanks, as far I could see there are ways to dynamically allocate resources (nextflow.io/docs/latest/…) but not detect threads, so this is a nice workaround.
  $endgroup$
  – TW93
  May 29 at 14:46
  

  
  
  
  

add a comment
 | 

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4

$begingroup$

I have not read the full Nextflow manual in depth, but I think there is no Nextflow command to detect the maximum number of threads you can use.

However, you can try to automatize this task by using the nproc command.

nproc gives you the number of processing units available. An idea would be to include something such nproc - 1 as the max number of threads for Roary.

share|improve this answer

edited May 29 at 13:57

terdon♦

5,82522 gold badges99 silver badges3333 bronze badges

answered May 29 at 12:20

platplat

74722 silver badges1212 bronze badges

$endgroup$

• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  Thanks, as far I could see there are ways to dynamically allocate resources (nextflow.io/docs/latest/…) but not detect threads, so this is a nice workaround.
  $endgroup$
  – TW93
  May 29 at 14:46
  

  
  
  
  

add a comment
 | 

4

$begingroup$

I have not read the full Nextflow manual in depth, but I think there is no Nextflow command to detect the maximum number of threads you can use.

However, you can try to automatize this task by using the nproc command.

nproc gives you the number of processing units available. An idea would be to include something such nproc - 1 as the max number of threads for Roary.

share|improve this answer

edited May 29 at 13:57

terdon♦

5,82522 gold badges99 silver badges3333 bronze badges

answered May 29 at 12:20

platplat

74722 silver badges1212 bronze badges

$endgroup$

• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  Thanks, as far I could see there are ways to dynamically allocate resources (nextflow.io/docs/latest/…) but not detect threads, so this is a nice workaround.
  $endgroup$
  – TW93
  May 29 at 14:46
  

  
  
  
  

add a comment
 | 

$begingroup$

I have not read the full Nextflow manual in depth, but I think there is no Nextflow command to detect the maximum number of threads you can use.

However, you can try to automatize this task by using the nproc command.

nproc gives you the number of processing units available. An idea would be to include something such nproc - 1 as the max number of threads for Roary.

share|improve this answer

edited May 29 at 13:57

terdon♦

5,82522 gold badges99 silver badges3333 bronze badges

answered May 29 at 12:20

platplat

74722 silver badges1212 bronze badges

$endgroup$

share|improve this answer

edited May 29 at 13:57

terdon♦

5,82522 gold badges99 silver badges3333 bronze badges

answered May 29 at 12:20

platplat

74722 silver badges1212 bronze badges

edited May 29 at 13:57

terdon♦

5,82522 gold badges99 silver badges3333 bronze badges

edited May 29 at 13:57

terdon♦

5,82522 gold badges99 silver badges3333 bronze badges

answered May 29 at 12:20

platplat

74722 silver badges1212 bronze badges

answered May 29 at 12:20

platplat

74722 silver badges1212 bronze badges