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Commits on Jan 31, 2018

• Merge pull request LangilleLab#22 from gavinmdouglas/run_pear_log

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• made input filename more obvious in error

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Commits on Jan 30, 2018

• Merge pull request LangilleLab#19 from gavinmdouglas/dada2_opt

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Commits on Jan 11, 2018

• Merge pull request LangilleLab#20 from gavinmdouglas/metaphlan2

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Commits on Nov 21, 2017

• changed bowtie2 default to be very-sensitive

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Commits on Nov 15, 2017

• added OMEGA_A and BAND_SIZE options

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Commits on Oct 31, 2017

• Merge pull request LangilleLab#18 from gavinmdouglas/filter_prop

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Commits on Oct 24, 2017

• Added filter_feature_table.R

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Commits on Oct 23, 2017

• Merge pull request LangilleLab#17 from gavinmdouglas/dada2_taxa

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Commits on Oct 18, 2017

• added random seed and allow taxa assignment skipping

  gavinmdouglas

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Commits on Oct 5, 2017

• Merge pull request LangilleLab#16 from gavinmdouglas/concat_string_match

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• added check for _1.fastq PE syntax and now sample name is taken to be first field after splitting by _

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Commits on Sep 27, 2017

• Merge pull request LangilleLab#15 from gavinmdouglas/tax_unclassified

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• added Unclassified as type of missing taxa

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• Merge pull request LangilleLab#13 from gavinmdouglas/dada2_scripts

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• Merge pull request LangilleLab#14 from gavinmdouglas/picrust_metadata

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• added script to add metadata to picrust precalc file

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• fixed how dada2 error plots are plotted

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Commits on Sep 26, 2017

• fixed bug where only forward err model used, added error plots, and made random seed optional

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• Output NA taxa levels as Unclassified

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• added check for non-numeric input parameters

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• made optparse lines easier to read

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Commits on Sep 25, 2017

• made parse_cutadapt_logs.py clarity changes and set input to be glob

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• minor changes to dada2_filter.R descriptions

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Commits on Sep 21, 2017

• added remaining script for dada2 pipeline

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• dada2_filter.R minor changes for clarity

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Commits on Sep 20, 2017

• changed Sample column to lowercase

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• fixed minor param log error

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• bug fixes for paired-end data

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• added first scripts for new workflow

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Commits on Jul 21, 2017

• Merge pull request LangilleLab#10 from LangilleLab/add-license-1

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Commits on Jul 20, 2017

• Allow input files to be gzipped. Output will then be gzipped as well.

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Commits on Jul 18, 2017

• Create LICENSE

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Commits on Jun 20, 2017

• Merge pull request LangilleLab#7 from gavinmdouglas/STAMP_ITS2_fix

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Commits on Jun 19, 2017

• fixed argparse typo in fix_ITS2_spf.py and only parsed for unidentified now

  

  Gavin Douglas

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