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Update of Ascat and INSTALL_BIANCA.md #628

Merged
merged 45 commits into from
Feb 1, 2019
Merged

Update of Ascat and INSTALL_BIANCA.md #628

merged 45 commits into from
Feb 1, 2019

Commits on Jun 1, 2017

  1. Merge remote branch 'upstream/master'

    Malin Larsson committed Jun 1, 2017
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Commits on Jun 7, 2017

  1. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 7, 2017
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Commits on Jun 12, 2017

  1. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  2. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  3. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  4. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  5. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  6. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  7. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  8. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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  9. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Jun 12, 2017
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Commits on Sep 7, 2017

  1. adding this file now

    Malin Larsson committed Sep 7, 2017
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  2. Merge branch 'master' of https://github.com/malinlarsson/CAW

    Malin Larsson committed Sep 7, 2017
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Commits on Apr 12, 2018

  1. Merge branch 'master' of https://github.com/malinlarsson/CAW 

    This is the first merge after renaming the upstream branch to Sarek.
Lots of changes compared with my previous version.
    malinlarsson committed Apr 12, 2018
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  2. Updated call to ascat.runAscat so that it uses gamma = 1, which is a … 

    …better setting when LogR and BAF measurements are based on NGS data
    malinlarsson committed Apr 12, 2018
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Commits on Aug 20, 2018

  1. Merge remote-tracking branch 'upstream/master'

    malinlarsson committed Aug 20, 2018
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Commits on Aug 21, 2018

  1. Merge remote-tracking branch 'upstream/master' 

    Incorporates recent changes in the documentation of the master project.
    Malin Larsson committed Aug 21, 2018
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Commits on Aug 22, 2018

  1. Update INSTALL_BIANCA.md 

    Added a specific example of how to run Ascat on GRCh37 on Bianca
    @malinlarsson
    malinlarsson authored Aug 22, 2018
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  2. Update INSTALL_BIANCA.md 

    Added info about the --containerPaths flag
    @malinlarsson
    malinlarsson authored Aug 22, 2018
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Commits on Aug 24, 2018

  1. Merge remote-tracking branch 'upstream/master'

    malinlarsson committed Aug 24, 2018
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  2. Merge branch 'master' of https://github.com/malinlarsson/Sarek

    malinlarsson committed Aug 24, 2018
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  3. updating Ascat. Set gamma to 1, and changed the content of the textfi… 

    …le xxxx.cnv.txt that contain the predicted CNV regions. The format of xxxx.cnv.txt is the same, but the change is that all segments are now written out, not only the ones with copy number != 2. This will make it easier to compare the figure xxxx.ASCATprofile with the textfile xxxx.cnv.txt. Now all regions in the figure are included in the text file. I have also updated the documentation to reflect these changes.
    malinlarsson committed Aug 24, 2018
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  4. updating Ascat doc

    malinlarsson committed Aug 24, 2018
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  5. Update ASCAT.md 

    small format update
    @malinlarsson
    malinlarsson authored Aug 24, 2018
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Commits on Aug 30, 2018

  1. Update ASCAT.md

    @malinlarsson
    malinlarsson authored Aug 30, 2018
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  2. Update ASCAT.md 

    More detailed description of the tumor.cnvs.txt file to explain that all segments are included in the file, also those with normal copy number.
    @malinlarsson
    malinlarsson authored Aug 30, 2018
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Commits on Oct 22, 2018

  1. updated ASCAT.md

    malinlarsson committed Oct 22, 2018
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  2. Merge remote-tracking branch 'upstream/master'

    malinlarsson committed Oct 22, 2018
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  3. fixed conflicts in ASCAT.md

    malinlarsson committed Oct 22, 2018
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  4. adding a gc correction step to Ascat

    malinlarsson committed Oct 22, 2018
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Commits on Oct 24, 2018

  1. fixed file extensions of pulled images

    malinlarsson committed Oct 24, 2018
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Commits on Dec 19, 2018

  1. Merge pull request nf-core#709 from SciLifeLab/dev 

    Release 2.2.2
    @maxulysse
    maxulysse authored Dec 19, 2018
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Commits on Jan 15, 2019

  1. Update ASCAT.md

    @malinlarsson
    malinlarsson authored Jan 15, 2019
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Commits on Jan 17, 2019

  1. Loci.gc files now in genome_base folder and the paths to these are pr… 

    …operly defined in genomes.config
    Malin Larsson committed Jan 17, 2019
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  2. Merge branch 'dev' into master

    @maxulysse
    maxulysse authored Jan 17, 2019
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  3. Remove cosmic

    @maxulysse
    maxulysse authored Jan 17, 2019
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  4. Update ASCAT.md

    @malinlarsson
    malinlarsson authored Jan 17, 2019
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  5. Update ASCAT.md 

    update of the documentation of how GC correction files were created
    @malinlarsson
    malinlarsson authored Jan 17, 2019
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  6. Update ASCAT.md 

    small updates
    @malinlarsson
    malinlarsson authored Jan 17, 2019
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  7. Update ASCAT.md

    @malinlarsson
    malinlarsson authored Jan 17, 2019
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  8. Update ASCAT.md

    @malinlarsson
    malinlarsson authored Jan 17, 2019
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Commits on Jan 23, 2019

  1. Update ASCAT.md

    @malinlarsson
    malinlarsson authored Jan 23, 2019
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Commits on Jan 31, 2019

  1. fixing conflicts

    Malin Larsson committed Jan 31, 2019
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  2. put back ascat gc correction files in genomes.config that I revoved i… 

    …n the merge
    Malin Larsson committed Jan 31, 2019
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  3. Merge branch 'master' of https://github.com/malinlarsson/Sarek

    Malin Larsson committed Jan 31, 2019
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