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Samplesheet multilevel nesting ick4#24

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Merged

jessicarowell merged 23 commits intomasterCDCgov/polkapox:masterfrom samplesheet_multilevel_nesting_ick4CDCgov/polkapox:samplesheet_multilevel_nesting_ick4Copy head branch name to clipboardJun 7, 2024

+250-213

Commits

Commits on Apr 5, 2024

• correct log to logger

  

  Jessica Rowell

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  1f5eea9

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• accept R_1/R_2 format in addition to R1/R2

  

  Jessica Rowell

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  7c3fc4b

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• remove function no lonnger using

  

  Jessica Rowell

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  96bd820

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• decided not to add the R_1/R_2 support

  

  Jessica Rowell

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  1dd42b4

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Commits on Apr 11, 2024

• modify samplesheet creator to handle multilevel file nesting

  

  Jessica Rowell

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  b899629

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• add the file_levels flag to nextflow pipeline

  

  Jessica Rowell

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  cdaf01e

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• don't pass null as a project_name and don't use the project_name flag is this param is empty

  

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  bc9fdeb

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Commits on Apr 12, 2024

• add file_levels param to schema

  

  Jessica Rowell

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Commits on Apr 18, 2024

• screate_samplesheet.py mods, check for file levels and run or error out

  

  Jessica Rowell

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Commits on Apr 22, 2024

• adding and correcting logic to file_levels param

  

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Commits on Apr 29, 2024

• update mpxgfa.sif location to point to staphb dockerhub polkapox repo

  

  Jessica Rowell

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Commits on Apr 30, 2024

• add missing comma

  

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Commits on May 2, 2024

• fix list index error in fix names fx

  

  Jessica Rowell

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  2329c31

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Commits on May 6, 2024

• fix dividing by strings error

  

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  eb9b4d3

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• add reqd module

  

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  d30c041

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Commits on May 7, 2024

• fix Index OOR error in get_raw_filt_counts by returning NA if file is not found

  

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  89d359b

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• avoid another index OOR error - get_kraken_stats

  

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  c4c8ded

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Commits on May 8, 2024

• overhaul the whole summarize_qc.py script

  

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  a9d4723

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Commits on May 9, 2024

• correction to the R1 R2 substitute regex

  

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  e51fc05

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• correct name of the pipeline

  

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  c7361f9

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Commits on May 30, 2024

• update documentation for multilevel samplesheet creation

  

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  25448cc

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Commits on May 31, 2024

• remove the file_levels=all option from create_samplesheet.py and documentation

  

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Commits on Jun 4, 2024

• enforce file levels in nextflow

  

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  7a8e39f

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