Module starindexgenerator uses all available cores about eoulsan HOT 3 CLOSED

Dear @AlbatrosHurleur,

Does this issue only affect the starindexgenerator step or all the others steps (e.g. the mapping step) of your workflow have the same issue?

I think that the following workaround can solve your issue by setting the requiredprocs attribute when configuring the starindexgenerator module/step:

        <!-- Create STAR index -->
        <step requiredprocs="32" skip="false">
                <module>starindexgenerator</module>
                <parameters>
                        <!-- The overhang value must be greater than the length of the reads -->
			<parameter>
				<name>overhang</name>
				<value>100</value>
			</parameter>
			<parameter>
				<name>use.gtf.file</name>
				<value>true</value>
			</parameter>
                        <parameter>
                                <name>gtf.feature.exon</name>
                                <value>exon</value>
                        </parameter>
                        <parameter>
                                <name>gtf.tag.exon.parent.transcript</name>
                                <value>Parent</value>
                        </parameter>
                </parameters>
        </step>

Best regards,
Laurent.

from eoulsan.

Dear @jourdren

Yes it affects only the starindexgenerator step; the rest of the steps use 32 cores as requested.

Indeed, adding requiredprocs="32" to the configuration solved this issue, thank you!
Would it be possible for this step to use the main.local.threads parameter in another version to come?

On another note, do you plan to make the newest versions of Eoulsan available from bioconda?

Thanks for your work on this project.

from eoulsan.

Dear @AlbatrosHurleur,

Great news that the workaround works for you.
I just fixed the issue with the fc37482 commit.

I will try to package Eoulsan in bioconda as soon as I publish the new Aozan [1,2] major release (3.0). Aozan is my other big project with ToulligQC.

Best regards,

Laurent.

[1] https://www.outils.genomique.biologie.ens.fr/aozan/
[2] https://github.com/GenomiqueENS/aozan/tree/branch-3.0

from eoulsan.