search

CCRGeneticsBranch / Oncogenomics_v2

Oncogenomics portal version 2
0 stars 0 forks source link

Test NF pipeline results #37

Open hsienchao opened 11 months ago

hsienchao commented 11 months ago

Just quickly checked case RMS2163/NFtest

In RMS2163_T1R_T3_HCNMNBGX7

  1. RMS2163_T1R_T3_HCNMNBGX7.final.squeeze.bam should be RMS2163_T1R_T3_HCNMNBGX7.star.final.squeeze.bam
  2. No RMS2163_T1R_T3_HCNMNBGX7.star.final.squeeze.bam.bai
  3. No RMS2163_T1R_T3_HCNMNBGX7.SJ.out.*
  4. RMS2163_T1R_T3_HCNMNBGX7.genes.results should be RMS2163_T1R_T3_HCNMNBGX7.rsem_ENS.genes.results
  5. No arriba_out

In RMS2163/db

  1. RMS2163.RNAseq should be RMS2163.rnaseq
  2. RMS2163.RNAseq and RMS2163.hotspot are empty
  3. No RMS2163.fusion.txt

In RMS2163/qc

  1. No multiqc_data
  2. No config.txt
hsienchao commented 9 months ago

looks good. I did not find squeeze.bam.bai. please copy it back. Yes we need SJ.out.tab.bed.gz for junction display. Once you fix these and config file, I can start syncing these to db.

vinegang commented 9 months ago

I added the squeeze.bam.bai and SJ.out.tab.bed.gz also now to the code base

vinegang commented 9 months ago

do we need config file in a specific format ..what elements are needed from the config. I am asking so that I will have the flexibility while coding it in

hsienchao commented 7 months ago

Changed the code to compatible with new NF expression file name.