Code

release 51.10 prep#226

Code

Merged

dozy merged 51 commits intomasterwtsi-npg/npg_seq_pipeline:masterfrom develwtsi-npg/npg_seq_pipeline:develCopy head branch name to clipboardJun 20, 2017

+403-3,221

Commits

Commits on Jan 23, 2017

• update sequencescape warehouse loader job

  mgcam

  committed
  aea45ef

Commits on Apr 26, 2017

• initial code deletion

  mgcam

  committed
  1d7c46f

Commits on May 11, 2017

• further code deletions and fixes to tests

  mgcam

  committed
  a58d062

• tests simplification

  mgcam

  committed
  bd8f809

Commits on May 15, 2017

• redirect stderr output to a log

  mgcam

  committed
  1a91fcd

Commits on May 17, 2017

• fix job id propagation

  mgcam

  committed
  204180b

Commits on May 18, 2017

• fixed bug in computing a path

  mgcam

  committed
  09d39d7

• remove gclp-specific code and conf. files

  mgcam

  committed
  591b8aa

• deleted illumina2bam function

  mgcam

  committed
  1559509

Commits on May 19, 2017

• ensure that error in the pipeline can be captured in the pipeline daemon log

  mgcam

  committed
  7a35555

Commits on May 23, 2017

• Merge pull request #218 from mgcam/stderr2log4perl_log

  Show description for 1b32f63
  

  Keith James

  authored
  1b32f63

Commits on May 24, 2017

• merged in wtsi/devel and resolved conflict in Changes file

  mgcam

  committed
  bba2b8e

• merged in wtsi/devel and resolved conflict in Changes file

  mgcam

  committed
  4916766

• merged in wtsi/devel and resolved conflict in Changes file

  mgcam

  committed
  3223aaa

• Merge remote-tracking branch 'wtsi/devel' into lims_sources4whloader

  mgcam

  committed
  d3ce9da

Commits on May 25, 2017

• update sequencescape warehouse loader job

  

  mgcam

  authored and

  dkj

  committed
  395fb2a

• Merge commit 'refs/pull/208/head' of https://github.com/wtsi-npg/npg_seq_pipeline into devel

  dkj

  committed
  cc63c83

Commits on Jun 5, 2017

• warn rather than croak in seq_alignemnt if multiple references for tag 0

  srl147

  committed
  b93f038

• allow p4 stage 1 to analyse runs with different length reads

  srl147

  committed
  a9521d0

• Chain execution of RNA-SeQC qc check to the vtfp/viv alignment cmd

  Show description for ff1b9d5
  

  Ruben E. Bautista

  committed
  ff1b9d5

• Remove use of attribute qc_report_dir for rna_seqc check

  Show description for 243d5d2
  

  Ruben E. Bautista

  committed
  243d5d2

• Fix bug - value of qc_in arg passed to rna_seqc is wrong in seq_alignment

  

  Ruben E. Bautista

  committed
  4337198

• Remove code that creates the BAM_basecalls_XX-XX/archive/qc/rna_seqc directory

  

  Ruben E. Bautista

  committed
  4e858e1

• Update seq_alignment tests to reflect latest changes

  

  Ruben E. Bautista

  committed
  fd7be64

• tests with multiple references

  mgcam

  committed
  622ca7c

• Update changelog and tidy up code

  Show description for e0d1233
  

  Ruben E. Bautista

  committed
  e0d1233

• Merge pull request #4 from mgcam/multiple_refs_in_alignment

  Show description for 0271e88
  srl147

  authored
  0271e88

• Merge pull request #223 from srl147/multiple_references

  Show description for 5502b4f
  mgcam

  authored
  5502b4f

• merged in wtsi/devel

  mgcam

  committed
  81ce476

• new merge for wtsi/devel and conflict resolution

  mgcam

  committed
  14edf1a

• merged in wtsi/devel and resolved conflict in Changes

  mgcam

  committed
  a00769a

• merged in wtsi/devel and resolved conflict in Changes

  mgcam

  committed
  1ccf4de

Commits on Jun 6, 2017

• Merge remote-tracking branch 'wtsi-ngp/devel' into different_length_reads

  Show description for cccfb34
  srl147

  committed
  cccfb34

• Merge pull request #224 from srl147/different_length_reads

  Show description for 924fe71
  mgcam

  authored
  924fe71

• Merge remote-tracking branch 'wtsi/devel' into less_olb

  Show description for e0492f4
  mgcam

  committed
  e0492f4

• Merge pull request #217 from mgcam/less_olb

  Show description for 2d4a62c
  srl147

  authored
  2d4a62c

• Merge remote-tracking branch 'wtsi/devel' into drop_gclp

  Show description for 54d1296
  mgcam

  committed
  54d1296

Commits on Jun 7, 2017

• Merge branch 'drop_il2b' of https://github.com/mgcam/npg_seq_pipeline into mgcam-drop_il2b

  Show description for a6dcbd7
  dozy

  committed
  a6dcbd7

• Merge branch 'mgcam-drop_il2b' into devel

  dozy

  committed
  a4d3506

• Merge remote-tracking branch 'wtsi/devel' into drop_gclp

  Show description for 3e5ec7b
  mgcam

  committed
  3e5ec7b

Commits on Jun 8, 2017

• removed unused force_p4 attribute from npg_pipeline/base.pm

  dozy

  committed
  ddb515d

• update Changes

  dozy

  committed
  0df06f9

• Merge pull request #4 from dozy/drop_gclp

  Show description for bfa9fb9
  mgcam

  authored
  bfa9fb9

• Merge pull request #219 from mgcam/drop_gclp

  Show description for a0867b7
  dozy

  authored
  a0867b7

• update p4 stage 2 (seq_alignment) to use bambi chrsplit instead of SplitBamByChromosomes.jar for Y-split runs

  dozy

  committed
  2049e9c

• update Changes

  dozy

  committed
  a00c3c5

• Tiny change: remove unused variable

  

  Ruben E. Bautista

  committed
  654c361

• extend list of names for chromosome Y for y-split to cover all variants in our current set of human reference genomes

  dozy

  committed
  e645566

• Merge branch 'devel' into rb11_rna_seqc_from_seq_alignment

  

  Ruben E. Bautista

  authored
  ade8b28

• Merge pull request #225 from dozy/ysplit_fixes

  Show description for 24e5163
  jenniferliddle

  authored
  24e5163

Commits on Jun 9, 2017

• Merge commit 'refs/pull/206/head' of https://github.com/wtsi-npg/npg_seq_pipeline into devel

  dkj

  committed
  fc2ad1e