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Fix the coverage report, we were using the samtools flags for decont. instead of mapping #8

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merged 11 commits into from
Jun 3, 2024
Merged

Fix the coverage report, we were using the samtools flags for decont. instead of mapping #8

merged 11 commits into from
Jun 3, 2024

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mberacochea
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Vkale1
Vkale1 reviewed May 30, 2024
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KateSakharova
KateSakharova approved these changes May 30, 2024
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Seems OK now

Ales-ibt
Ales-ibt requested changes May 30, 2024
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Thank you for this. I think we should consider the solutions we have implemented in other pipelines and modules to minimise the storage of bam files for decontamination and alignment steps.

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@mberacochea mberacochea self-assigned this Jun 3, 2024
@mberacochea mberacochea requested a review from Ales-ibt June 3, 2024 12:57
KateSakharova
KateSakharova reviewed Jun 3, 2024
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Ales-ibt approved these changes Jun 3, 2024
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Thank you for changing the decontamination module :D

@mberacochea mberacochea merged commit 947ce07 into main Jun 3, 2024
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@mberacochea mberacochea deleted the bugfix/coverage_report branch June 3, 2024 15:24
@mberacochea mberacochea restored the bugfix/coverage_report branch June 3, 2024 15:51
@KateSakharova KateSakharova deleted the bugfix/coverage_report branch June 4, 2024 15:14
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@KateSakharova KateSakharova KateSakharova approved these changes

@Vkale1 Vkale1 Vkale1 left review comments

@Ales-ibt Ales-ibt Ales-ibt approved these changes

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@mberacochea @Ales-ibt @Vkale1 @KateSakharova