Code

Add optional merging and trimming#142

Code

Merged

apeltzer merged 56 commits intonf-core:ar_optionalnf-core/eager:ar_optionalfrom maxibor:devCopy head branch name to clipboardMar 4, 2019

+262-90

Commits

Commits on Feb 1, 2019

• Extra clarifications for indices, FastP and general cleanup

  jfy133

  authored
  eb59405

• Merge pull request #136 from nf-core/help_message_improvements

  Show description for df6305f
  apeltzer

  authored
  df6305f

Commits on Feb 2, 2019

• Further clarification on --max-cpus

  Show description for f43f4b0
  jfy133

  authored
  f43f4b0

• Update docs/usage.md

  Show description for 45ce547
  

  apeltzer

  and

  jfy133

  authored
  45ce547

• Merge pull request #139 from nf-core/docs_update

  Show description for e039f28
  apeltzer

  authored
  e039f28

Commits on Feb 11, 2019

• add noCollase option

  maxibor

  committed
  91d05cb

• fix nf-PE read index

  maxibor

  committed
  758fb7f

• update doc with noCollapse

  maxibor

  committed
  e2aaba0

• merge master to dev

  maxibor

  committed
  bdd56dc

• main.nf to dev

  maxibor

  committed
  55743dd

• fix funky prefix

  maxibor

  committed
  8ec9d67

• Update docs/usage.md

  Show description for 6d864e1
  

  apeltzer

  and

  maxibor

  authored
  6d864e1

Commits on Feb 12, 2019

• Update docs/usage.md

  Show description for f3a6ff7
  

  apeltzer

  and

  maxibor

  authored
  f3a6ff7

• skip trimming and collapsing

  maxibor

  committed
  0e03a00

• update test

  maxibor

  committed
  757e930

Commits on Feb 19, 2019

• Address issue with picard memory

  apeltzer

  committed
  949fd28

• Merge pull request #145 from apeltzer/fix-picard

  Show description for 435812b
  apeltzer

  authored
  435812b

Commits on Feb 21, 2019

• Use CSI indices wherever possible

  apeltzer

  committed
  b311d61

• Merge remote-tracking branch 'upstream/dev' into fix-samtools-idx

  apeltzer

  committed
  a1a69a7

• Add proper changelog

  apeltzer

  committed
  9eb36c7

• Added a contributor section to README

  apeltzer

  committed
  8d26b33

• Update README.md with instructions for test data

  evanfloden

  authored
  8e29eff

• Merge pull request #148 from evanfloden/patch-1

  Show description for 8f3c151
  apeltzer

  authored
  8f3c151

• Add docs on this

  apeltzer

  committed
  abf4642

Commits on Feb 25, 2019

• Update new parameter large_ref

  apeltzer

  committed
  8a6dccb

• Fixing indices hopefully

  apeltzer

  committed
  b6f65b1

• Fixing indexing

  apeltzer

  committed
  f9ac1d4

• Fix for post-dup steps

  apeltzer

  committed
  7405c8e

• Nicer changelog [skip ci]

  apeltzer

  committed
  7e4035d

• Its unpublished stuff [skip ci]

  apeltzer

  committed
  76e0cbd

• Merge pull request #3 from nf-core/dev

  Show description for a2364b4
  jfy133

  authored
  a2364b4

• Made polyG param clearer what it is

  jfy133

  authored
  e971cac

• Update CHANGELOG.md

  jfy133

  authored
  0feeb19

• Updated ploy G trim flag

  jfy133

  authored
  29306df

• Merge pull request #5 from jfy133/polyg-name-improvements

  Show description for 028f7ea
  jfy133

  authored
  028f7ea

• Update CHANGELOG.md

  jfy133

  authored
  bc02be2

• Merge pull request #4 from jfy133/polyg-name-improvement

  Show description for ffa0085
  jfy133

  authored
  ffa0085

• Update CHANGELOG.md

  jfy133

  authored
  7836ab8

• Added fastP position to MultiQC config

  jfy133

  authored
  6d13545

Commits on Feb 26, 2019

• Merge pull request #147 from apeltzer/fix-samtools-idx

  Show description for ee3c44f
  apeltzer

  authored
  ee3c44f

• Merge branch 'dev' into fix-post-dedup-steps

  apeltzer

  authored
  0fb1481

• Should fix the remaining issues

  apeltzer

  committed
  fabd1a3

• Merge branch 'fix-post-dedup-steps' of https://github.com/apeltzer/eager into fix-post-dedup-steps

  apeltzer

  committed
  24ea4b7

• Address issues with qualimap / multiqc / multiple samples and reporting

  apeltzer

  committed
  c69261d

Commits on Feb 27, 2019

• Merge pull request #151 from apeltzer/fix-post-dedup-steps

  Show description for e85b58f
  apeltzer

  authored
  e85b58f

• Merge branch 'dev' into dev

  apeltzer

  authored
  16fedae

• Merge pull request #152 from jfy133/dev

  Show description for 71f0329
  apeltzer

  authored
  71f0329

Commits on Mar 1, 2019

• Adding in publishing dedup log files as well

  apeltzer

  committed
  817b9e0

Commits on Mar 2, 2019

• Merge pull request #157 from apeltzer/publish_dedup

  Show description for 5a255fd
  apeltzer

  authored
  5a255fd

Commits on Mar 4, 2019

• Merge branch 'dev' into dev

  apeltzer

  authored
  c0251cb

• move size out of the if clause

  apeltzer

  committed
  3320464

• match skip_* pattern

  maxibor

  committed
  def1b35

• update travis test

  maxibor

  committed
  2bef839

• local executor for skipping AR process

  maxibor

  committed
  e62b503

• initialize skip_adapterremoval

  maxibor

  committed
  e807c58

• fix bam test

  maxibor

  committed
  01d056c