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Master - Monthly merge from Develop #159

Merged
merged 57 commits into from

4 participants

@vals

Key changes

  • nophix name handling
  • Project pruning at flowcell level
  • project_analysis_setup is now called project_management
  • Name parsing has been updated to accommodate agilent and rna barcodes
  • A 'backup' task has been added
  • Manually entered comments in the project read counts worksheets in google docs are now preserved across updates.
  • There also are no longer comment and pass columns in the gdocs project reports.
  • OLB 1.9 location file format support has been added.
  • A framework for converting Complete Genomics structural variant events to VCF has been added.
  • Fastq files will now be created even if the directory exists.
  • Glob to find filtered sequence files have been improved.
  • The --compress option have been removed from rsync transfer to speed up file transfer.
  • Mondrain indexes are now parsed.

For finer detail in changes, see all the commits from a0fe27c up to this commit.

percyfal and others added some commits
@percyfal percyfal Handle nophix names nicely a0fe27c
@percyfal percyfal Merge branch 'develop' of git://github.com/SciLifeLab/bcbb into develop a568b30
@percyfal percyfal Add project pruning at flowcell level e89b175
@vals vals Made a helper function that tries doing float conversion
but reverts to the given string in case it cannot be converted to float.
Also handles formatting in this function.
253ac96
@percyfal percyfal Rename project_analysis_setup to more generic project_management e65bebf
@percyfal percyfal Merge branch 'develop' of git://github.com/SciLifeLab/bcbb into develop 39ffea2
@chapmanb chapmanb Merge pull request #56 from vals/brads-master
Fix for localization and parsing error
62af537
@percyfal percyfal Modify data delivery directory. Customer delivery goes to project_dir…
…/project_name/fc_id
23187bf
@percyfal percyfal Merge branch 'develop' of git://github.com/SciLifeLab/bcbb into develop 7aea7cc
@percyfal percyfal Update project_management 5806029
@percyfal percyfal add module scilifelab a6412e7
@percyfal percyfal Remove project_analysis_setup.py 252fac1
@percyfal percyfal Remove fc_delivery_report c1ab6fa
@percyfal percyfal Modify installed files aeb4edc
@vals vals Merge pull request #144 from percyfal/develop
Develop - move project based analysis
e44df4a
@b97pla b97pla updated name parsing to accommodate agilent and rna barcodes 8e0a1b9
@b97pla b97pla Merge pull request #145 from b97pla/develop
Develop
55d5d63
@b97pla b97pla added backup task a435428
@b97pla b97pla removed accidentally committed experimental code f8bf8f2
@b97pla b97pla Merge branch 'develop' of github.com:SciLifeLab/bcbb into develop d39c7a9
@b97pla b97pla no genomes_filter_out option by default 732b4ce
@b97pla b97pla dont use sample-level description 063869e
@b97pla b97pla Merge branch 'feature/no_genomes_filter_out' into develop 1e6527f
@vals vals PEP8 formatting a9e0786
@vals vals Only try to grab parent folder title in create_project_report_on_gdoc…
…s() if there is one.

Fixes #149.
61654b9
@vals vals Merge pull request #150 from vals/develop
Develop - Fixes #149
31a8bb6
@chapmanb chapmanb Initial framework for converting Complete Genomics structural variant…
… events to VCF
171aa95
@chapmanb chapmanb Merge branch 'master' of github.com:chapmanb/bcbb 7785aff
@b97pla b97pla Merge branch 'develop' of github.com:SciLifeLab/bcbb into develop af25a6a
@b97pla b97pla added check to skip qseq to fastq conversion if outfile exists e63a27e
@vals vals (PEP8 formatting) b1c7e72
@vals vals Removed the comment and pass field from gdocs project report 5d4c3e5
@chapmanb chapmanb Handle new location file format for OLB 1.9 e997938
@vals vals No longer reading the non existant data from the spreasheets f8232e2
@vals vals Saving comment and pass status from Summary worksheet 1ca030c
@vals vals Handle if the summary doesn't exist for some sample name or project abe4c2d
@vals vals Merging from upstream c328329
@vals vals Merge pull request #152 from vals/develop
Develop - Google docs changes, fixes #58
50fdc8a
@chapmanb chapmanb Update query example to match paper text ad08d5d
@chapmanb chapmanb Merge branch 'master' of github.com:chapmanb/bcbb 8b576ea
@chapmanb chapmanb Support haploid calling, background VCF input and specific target reg…
…ions as part of freebayes variant calling
5057374
@vals vals Merge remote-tracking branch 'brad/master' into develop 3a8648c
@vals vals silly formating f9f5971
@b97pla b97pla create fastq files even if directory exists 94b5451
@vals vals Merge pull request #153 from b97pla/develop
Develop
31e2dd1
@vals vals Merge remote branch 'central/develop' into develop 25a93cd
@vals vals Adding mosaik_index.loc, which failed to come with a merge cd094c8
@vals vals Changing variantcall test to use BWA 53fffe3
@vals vals Merge pull request #154 from vals/develop
Develop - Merge from upstream
79fac54
@b97pla b97pla more specific glob to find already filtered sequence files 27bf4b0
@vals vals merge conflict due to scilifelab submodule 9448666
@vals vals Merge remote-tracking branch 'central/develop' into develop 67e1cdf
@vals vals Removed the --compress option in the rsync transfer, fixes issue #155 d1077b7
@vals vals Merge pull request #156 from vals/develop
Develop - Removing '--compression' from rsync transfer.
262664f
@b97pla b97pla Merge branch 'develop' of github.com:SciLifeLab/bcbb into develop 658f0b1
@b97pla b97pla added parsing of mondrian indexes a3d32ec
@vals vals Merge pull request #158 from b97pla/develop
Develop
1aa74dc
@vals vals merged commit d8a217d into master
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Commits on Mar 29, 2012
  1. @percyfal

    Handle nophix names nicely

    percyfal authored
  2. @percyfal
Commits on Mar 30, 2012
  1. @percyfal
Commits on Apr 2, 2012
  1. @vals

    Made a helper function that tries doing float conversion

    vals authored
    but reverts to the given string in case it cannot be converted to float.
    Also handles formatting in this function.
Commits on Apr 3, 2012
  1. @percyfal
  2. @percyfal
  3. @chapmanb

    Merge pull request #56 from vals/brads-master

    chapmanb authored
    Fix for localization and parsing error
  4. @percyfal
Commits on Apr 5, 2012
  1. @percyfal
  2. @percyfal

    Update project_management

    percyfal authored
Commits on Apr 12, 2012
  1. @percyfal

    add module scilifelab

    percyfal authored
  2. @percyfal
  3. @percyfal

    Remove fc_delivery_report

    percyfal authored
  4. @percyfal

    Modify installed files

    percyfal authored
  5. @vals

    Merge pull request #144 from percyfal/develop

    vals authored
    Develop - move project based analysis
  6. @b97pla
  7. @b97pla

    Merge pull request #145 from b97pla/develop

    b97pla authored
    Develop
  8. @b97pla

    added backup task

    b97pla authored
  9. @b97pla
Commits on Apr 16, 2012
  1. @b97pla
  2. @b97pla
  3. @b97pla
  4. @b97pla
Commits on Apr 17, 2012
  1. @vals

    PEP8 formatting

    vals authored
  2. @vals

    Only try to grab parent folder title in create_project_report_on_gdoc…

    vals authored
    …s() if there is one.
    
    Fixes #149.
  3. @vals

    Merge pull request #150 from vals/develop

    vals authored
    Develop - Fixes #149
Commits on Apr 18, 2012
  1. @chapmanb
  2. @chapmanb
  3. @b97pla
  4. @b97pla
Commits on Apr 19, 2012
  1. @vals

    (PEP8 formatting)

    vals authored
  2. @vals
Commits on Apr 20, 2012
  1. @chapmanb
  2. @vals
  3. @vals
  4. @vals
  5. @vals

    Merging from upstream

    vals authored
  6. @vals

    Merge pull request #152 from vals/develop

    vals authored
    Develop - Google docs changes, fixes #58
Commits on Apr 30, 2012
  1. @chapmanb
  2. @chapmanb
Commits on May 2, 2012
  1. @chapmanb

    Support haploid calling, background VCF input and specific target reg…

    chapmanb authored
    …ions as part of freebayes variant calling
  2. @vals
Commits on May 3, 2012
  1. @vals

    silly formating

    vals authored
  2. @b97pla
Commits on May 4, 2012
  1. @vals

    Merge pull request #153 from b97pla/develop

    vals authored
    Develop
  2. @vals
  3. @vals
  4. @vals
  5. @vals

    Merge pull request #154 from vals/develop

    vals authored
    Develop - Merge from upstream
Commits on May 8, 2012
  1. @b97pla
Commits on May 10, 2012
  1. @vals
  2. @vals
  3. @vals
  4. @vals

    Merge pull request #156 from vals/develop

    vals authored
    Develop - Removing '--compression' from rsync transfer.
Commits on May 11, 2012
  1. @b97pla
  2. @b97pla
  3. @vals

    Merge pull request #158 from b97pla/develop

    vals authored
    Develop
Something went wrong with that request. Please try again.