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Add resources (e.g. mem usage) to each rule #7

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Maarten-vd-Sande opened this issue Jul 23, 2019 · 6 comments
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Add resources (e.g. mem usage) to each rule #7

Maarten-vd-Sande opened this issue Jul 23, 2019 · 6 comments
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enhancement New feature or request stale Period of inactivity

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@Maarten-vd-Sande
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Based on bechmark results?
#5
@Maarten-vd-Sande Maarten-vd-Sande mentioned this issue Jul 23, 2019
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@Maarten-vd-Sande Maarten-vd-Sande added the enhancement New feature or request label Jul 23, 2019
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stale bot commented Aug 28, 2019

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

@stale stale bot added the stale Period of inactivity label Aug 28, 2019
@Maarten-vd-Sande
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Yes this is still relevant!

@stale stale bot removed the stale Period of inactivity label Aug 28, 2019
@Maarten-vd-Sande Maarten-vd-Sande added this to the First release milestone Aug 31, 2019
@Maarten-vd-Sande Maarten-vd-Sande mentioned this issue Sep 1, 2019
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@siebrenf
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Added several resources for rules used in rna-seq #167 :

memory usage:

  • salmon
  • star
  • samtools_sort
  • mark_duplicates

other bottlenecks:

  • deeptools=1 (doesn't run in parallel)
  • parallel_downloads=1 (was already set by Maarten)

Values originated from benchmarks run on samples mapped to the human genome.
Trimming rules and samtools_index had a negligible memory usage.

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stale bot commented Oct 17, 2019

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

@stale stale bot added the stale Period of inactivity label Oct 17, 2019
@siebrenf siebrenf removed the stale Period of inactivity label Oct 18, 2019
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stale bot commented Nov 15, 2019

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

@stale stale bot added the stale Period of inactivity label Nov 15, 2019
@Maarten-vd-Sande Maarten-vd-Sande removed the stale Period of inactivity label Dec 3, 2019
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stale bot commented Dec 31, 2019

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

@stale stale bot added the stale Period of inactivity label Dec 31, 2019
@stale stale bot closed this as completed Jan 21, 2020
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@Maarten-vd-Sande @siebrenf