Tidy up

[erikwaskiewicz]

A few bits that could be tidied up but not critical (I'm probably just being picky)

1_SomaticFusion

• SomaticFusion/1_SomaticFusion.sh

  Line 35 in 5f83964

  vendorCaptureBed=./180702_HG19_PanCancer_EZ_capture_targets.bed

  • These variables aren't used

• SomaticFusion/1_SomaticFusion.sh

  Line 74 in 5f83964

  sampleId_without_conc="$(echo $sampleId | cut -d'_' -f1)"

  • Remove the underscores from sample ids

• SomaticFusion/1_SomaticFusion.sh

  Line 117 in 5f83964

  /home/transfer/miniconda3/envs/SomaticFusion/lib/STAR-Fusion/FusionInspector/FusionInspector --fusions star-fusion.fusion_predictions.abridged.coding_effect.tsv --out_prefix finspector --min_junction_reads 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --vis --max_promiscuity 10 --out_dir /share/data/results/"$seqId"/RocheSTFusion/"$sampleId"/STAR-Fusion/FusionInspector-validate --genome_lib_dir /share/apps/star-fusion/GRCh37_gencode_v19_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir/ --CPU 12 --samples_file /share/data/results/"$seqId"/RocheSTFusion/"$sampleId"/STAR-Fusion/starF.target_samples.txt --include_Trinity --annotate --examine_coding_effect --require_LDAS 0

  • Wrap over multiple lines?

• SomaticFusion/1_SomaticFusion.sh

  Line 477 in 5f83964

  grep -A 100 "^Sample_ID" SampleSheet.csv >> samples.csv

  • Make a really big number, just in case we do >100 samples in the future

• HsMetrics and alignment summary files from run folder could be put into the sample folders to tidy up a bit

make_fusion_report.py

• SomaticFusion/make-fusion-report.py

  Line 132 in 5f83964

  right_breakpoint = sfln[8]

  • Duplicate of line 122

contamination scripts

• SomaticFusion/contamination_check_arriba.py

  Line 36 in 5f83964

  NTC_in_sample= ("NTC" in sample)

  • use "NTC" in sample.upper() - will catch if NTC has accidentally been named ntc or Ntc etc...
  • I think this is in all the contamination scripts

Referrals

• Move referrals folder into RocheSTFusion folder

[erikwaskiewicz]

Extra bit from code review in #5 - add more comments to make_worksheets.py
Basically anywhere there there's a few empty lines between sections of code, add a quick comment for each block