Adding multithreading option for cutadapt and demultiplex sub commands

[skchronicles]

cutadapt with multiple threads

About
Cutadapt versions greater than or equal to 1.15 support multithreading, adding an option to run cutadapt in this mode.

Changes
This option is only enabled if the version of cutadapt in the user's PATH is greater than or equal to 1.15. Under the hood, I am checking for compatibility with the minimum version of cutadapt that is supported against the version of cutadapt in the user's path. If the version of cutadapt that is install does not support the -j option, then it is not provided at command line (i.e. meaning it will run the same as before).

Unit-tests were added to ensure everything is producing the expected outputs.

[CLAassistant]

All committers have signed the CLA.

[skchronicles]

Hey @tomazc,

I hope you are having a great day, and that you are staying safe in these strange times. Thank you for creating and maintaining this awesome tool!

My team is using iCount in a pipeline we are developing. I am working with pretty high coverage samples so speed up the run time of the demultiplex and/or cutadapt sub command, I have added a new option to enable multithreading. This option is only added to the cutadapt command if the version of cutadapt in the user's path supports multithreading (i.e. version>=1.15).

I was just wondering if you had time to look this over. Please let me know what you think. Thank you for your time, and have a wonderful day!

Best regards,
@skchronicles

[skchronicles]

Hey @tomazc,

I can confirm that everything works as expected.

Here are some jobs I submitted with the new --threads option. It is now using multiple threads for the cutadapt and demultiplex sub commands:

iCount cutadapt

iCount demultiplex

I also built a docker image for the tool if anyone else wants to use this latest version of the tool:

• https://hub.docker.com/r/nciccbr/ccbr_icount