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TODO.md

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TODO LIST

URGENTI

  • Ordina files pipelines per uso/importanza
  • Tolgiere pipeline di test
  • Identifica file di annotazione per BAITS e TARGETS a partire dal campo Recipe del samplesheet.

PIPELINE DA AGGIUNGERE

  • FlipFLop e alternative splicing (LONG TERM)

COSE DA SISTEMARE

  • rseqc: geneBodyCoverage e' la morte, lanciare in parallelo e mergiamo le linee di R in un report custom (knitr) facendo una HEATMAP se ci sono > 10 campioni
  • SampleSheet parser per Rapid Run
  • FINALIZZARE rnaseq report

TEST PER RNASEQ

  • /lustre2/scratch/Gentner/175_Induced_Leukemias

  • /lustre2/raw_data/T_140918_SN859_0178_AC42L6ACXX/Project_Gentner_175_Induced_leukemias/

/lustre2/raw_data/141104_SN859_0184_AC4863ACXX/Project_Gentner_175_Induced_leukemias/

TODO LIST OLD

  • TRIGGERS partendo da fastqc with send (fail)

  • BRANCH variables

  • BAM RECALIBRATION splittando i bam per chromosome? see docs PICMEGRE

  • Add triggers for quality (fail pipeline if quality is low) (with FAIL or WARN)