Merge branch 'patch-flexiprep-parse-adapters' into 'develop'
Patch flexiprep parse adapters This addresses the bug (not reported) where the adapters are incorrectly supplied to cutadapt. To protect against it, unit tests were added, and some refactoring was done. See merge request !82
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- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 16 additions, 14 deletions...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
- public/flexiprep/pom.xml 12 additions, 0 deletionspublic/flexiprep/pom.xml
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala 2 additions, 2 deletions...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala 130 additions, 58 deletions...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala 1 addition, 1 deletion...mc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
- public/flexiprep/src/test/resources/fqc_contaminants_v0101.txt 170 additions, 0 deletions...c/flexiprep/src/test/resources/fqc_contaminants_v0101.txt
- public/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt 838 additions, 0 deletions...xiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
- public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala 80 additions, 0 deletions...umc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
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