Move parameters to configuration file, add run script#4

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erflynn wants to merge 20 commits intomainfrom

Commits on Nov 10, 2021

Moved params and container paths to external config file
erflynn
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Commits on Nov 17, 2021

added run script and increased time for processes to allow full sample run
erflynn
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Commits on Dec 8, 2021

added code for testing comparisons
erflynn
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Commits on Dec 17, 2021

updated to new index, no ribo quenching
erflynn
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Commits on Jan 12, 2022

cleaned up files to remove rrna extra steps and paths
erflynn
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Commits on Jan 17, 2022

added code for running kallisto to pipeline
erflynn
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Commits on Jun 6, 2022

Commits on Jun 7, 2022

Commits on Jun 27, 2022

write out unfiltered file
erflynn
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Commits on Aug 11, 2022

updated to analysis set reference
erflynn
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Commits on Aug 14, 2022

working full version w new ref
erflynn
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