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Fix/fix preprocessing 20211119#9

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cschu wants to merge 36 commits intomasterzellerlab/gaga2:masterfrom fix/fix_preprocessing_20211119zellerlab/gaga2:fix/fix_preprocessing_20211119Copy head branch name to clipboard

+278-135

Commits

Commits on Nov 10, 2021

• added preprocessing of raw reads

  cschu

  committed
  dddfc9c

• version bump -> 0.4

  cschu

  committed
  e187ad6

• added --preprocessed flag + changed flow-logic; minor cleanup

  cschu

  committed
  b229a70

• Update README.md

  cschu

  authored
  c0727c7

• fixed some that would generate the wrong table format when having a single sample

  cschu

  committed
  31cd58b

• Added support for different R1/R2 lengths

  Show description for 2c089d2
  cschu

  committed
  2c089d2

Commits on Nov 11, 2021

• cleanup

  cschu

  committed
  b80eaaa

• added bbduk label

  cschu

  committed
  56a6a6d

• readlen homogenisation is now done by bbduk; added bbduk/dada2 labels

  cschu

  committed
  192e030

• tidy directories

  cschu

  committed
  ab67729

• added missing curly bracket

  cschu

  committed
  8b049da

• added mapseq-profiling of asv sequences

  cschu

  committed
  a21e31f

• added docs folder

  cschu

  committed
  5edcff8

• Add files via upload

  Show description for 46b3ec9
  cschu

  authored
  46b3ec9

• Update README.md

  Show description for ec96e3b
  cschu

  authored
  ec96e3b

Commits on Nov 17, 2021

• added parameters for dada2 chimera removal

  cschu

  committed
  0c78457

• Merge branch 'feature/add_preprocessing' of https://github.com/zellerlab/gaga2 into feature/add_preprocessing

  cschu

  committed
  91d0038

Commits on Nov 18, 2021

• removed vortex-code (prevalence check) as it fails for certain samples

  cschu

  committed
  75429dd

Commits on Nov 19, 2021

• Update flow diagram

  cschu

  authored
  4c996cb

• removed accidentally created file

  cschu

  committed
  da64390

• added illumina 16S technical sequences

  cschu

  committed
  ebf395d

• changed read length assessment

  Show description for d413236
  cschu

  committed
  d413236

• changed adapter/primer removal to 2-step fwd/rev clipping

  cschu

  committed
  6676044

• main workflow changes

  Show description for e1a824e
  cschu

  committed
  e1a824e

• version bump -> 0.4.1

  cschu

  committed
  416d79b

• Merge branch 'master' into fix/fix_preprocessing_20211119

  cschu

  authored
  2801221

• Update README.md

  cschu

  authored
  277b56d

• Update README.md

  cschu

  authored
  6ee07ba

• fixed post-merge main.nf

  cschu

  committed
  66bb7ce

Commits on Nov 22, 2021

• increased run time for dada2 processes, added custom mapseq db

  cschu

  committed
  38858f0

• changed mapseq output to simple, allowed custom mapseq databases

  cschu

  committed
  4aecd92

Commits on Nov 24, 2021

• changed publish_mode to copy, upped memory for dada2, added custom mapseq db

  cschu

  committed
  9a35410

• improved read length resolution during assessment

  Show description for 8eddf2c
  cschu

  committed
  8eddf2c

• added stepwise read preprocessing, individually cleaning r1/r2 from adapters/primers

  cschu

  committed
  a716191

• various changes to preprocessing/data flow

  Show description for 7a1c483
  cschu

  committed
  7a1c483

• added --long_reads documentation

  cschu

  committed
  35cf558