Update to Innuca's recipe modules#191

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cimendes wants to merge 20 commits intodevfrom

Commits on Jan 8, 2019

integrity_coverage template now checks the integrity of the read files with the appropriate compressing software. Added new directive with container
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Commits on Jan 9, 2019

Commits on Jan 10, 2019

add insert_size template
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Commits on Jan 11, 2019

added new retry to re-filter only by gc if assembly size is lower than the 80% threshold.
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verifies the % of mapped reads, issuing an warning when it falls
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Commits on Jan 14, 2019

new container directive for mlst process.
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Commits on Jan 15, 2019

fix typo
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Commits on Jan 16, 2019

update true_coverage image
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Commits on Jan 22, 2019

Commits on Jan 26, 2019

code cleanup
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Commits on Feb 6, 2019

Update to fastQC rules for emitting warning and fail messages.
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