- Nov 08, 2015
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Peter van 't Hof authored
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- Nov 07, 2015
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Peter van 't Hof authored
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- Nov 06, 2015
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Peter van 't Hof authored
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- Nov 05, 2015
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Peter van 't Hof authored
Fix gentrap report pdf See merge request !266
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Peter van 't Hof authored
Fix VEP `--failed` flag the `failed` flag should be a flag per the documentation (see: http://grch37.ensembl.org/info/docs/tools/vep/script/vep_options.html, and http://oct2014.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html ) But, when running, it requires a numeric value. When running the VEP with verbose mode, it appears that all boolean flags get converted to 1. Therefore, I'm setting `failed` to have value 1. This bug has been reported to Ensembl. It occurs in all versions, including most recent version 82. @p.j.van_t_hof Should we include a failback mode, in case Ensembl fixes this in version 83? See merge request !267
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- Nov 04, 2015
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Sander van der Zeeuw authored
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Sander van der Zeeuw authored
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Sander van der Zeeuw authored
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- Nov 03, 2015
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Wai Yi Leung authored
Fix gears parse Fixed small parse bug for the report See merge request !265
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Wai Yi Leung authored
Added a default for the retry arg Small option to add retry by default, also can use the config to set retries now See merge request !264
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Peter van 't Hof authored
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Peter van 't Hof authored
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- Nov 02, 2015
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Sander Bollen authored
Fix shiva fails This branch will be used to fix found issues while running functional testing of shiva. - [x] Fix report when not executing multisamplecalling - [x] Fix missing key when no indelrealignment and base recalibration in summary - [x] Fix wrong sample flag for single sample variant calling - [x] Fix name of link when sample has only 1 lib - [x] Added settings to Shiva summary - [x] Raise default memory - [x] Fix concordance checks See merge request !261
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Peter van 't Hof authored
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Peter van 't Hof authored
Conflicts: public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
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Peter van 't Hof authored
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Sander Bollen authored
the `failed` flag should be a flag per the documentation (see: http://grch37.ensembl.org/info/docs/tools/vep/script/vep_options.html, and http://oct2014.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html ) But, when running, it requires a numeric value. When running the VEP with verbose mode, it appears that all boolean flags get converted to 1. Therefore, I'm setting `failed` to have value 1.
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Sander Bollen authored
Refactoring of gears @wyleung @h.mei Resolves #219, #165 and #232 Features to be added: * [x] Kraken-report to JSON -> for html Sunflare plot display * [x] R2, distinguish Single End or Paired End, this is used in Kraken for pairing and possible downstream alignments * [x] Kraken-json to summary-json * ~~[ ] Add bedtools genomecoverage (or similar tool to determine horizontal coverage and output bedgraph/wiggle)~~ * [x] Support for RNA aligners aligned bams, these may contain multiple alignments for 1 sequence. SamToFastq is not handling this. * [x] Add report (sunflare plot) * [x] Add tests See merge request !241
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Peter van 't Hof authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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- Oct 31, 2015
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Peter van 't Hof authored
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- Oct 30, 2015
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Peter van 't Hof authored
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Peter van 't Hof authored
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Wai Yi Leung authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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- Oct 29, 2015
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Wai Yi Leung authored
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Peter van 't Hof authored
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Sander Bollen authored
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Sander Bollen authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Wai Yi Leung authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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