Skip to content

Latest commit

 

History

History
65 lines (46 loc) · 2.38 KB

08_cleanup.md

File metadata and controls

65 lines (46 loc) · 2.38 KB

08 - Cleanup

Created: 2022/11/17 14:50:49 Last modified: 2023/02/28 15:12:49

  • Aim: This document documents/describes cleaning up
  • Prerequisite software: GNU coreutils, singularity v3.7.2-1.el7, slurm v20.11.6
  • OS: ORAC (CentOS Linux) (ESR production network)

Table of contents

Cleanup and backup

rm -r ./fastq/

rm -rf ./logs/

rm -rf ./scripts/

rm -rf ./config/

rm -rf ./docs/

rm .gitignore

rm -rf .git/

rm -rf ./results/03_pipeline_runs/cohort/fastq/
rm -rf ./results/03_pipeline_runs/singleton/fastq/

rm -rf ./results/03_pipeline_runs/*/*_pipeline/config/
rm -rf ./results/03_pipeline_runs/*/*_pipeline/workflow/
rm -rf ./results/03_pipeline_runs/*/*_pipeline/images/
rm -rf ./results/03_pipeline_runs/*/*_pipeline/docs/
rm -rf ./results/03_pipeline_runs/*/*_pipeline/test/
rm -rf ./results/03_pipeline_runs/*/*_pipeline/README.md

rm -rf ./results/03_pipeline_runs/*/*_pipeline/results/README.md
rm -rf ./results/03_pipeline_runs/*/human_genomics_pipeline/results/trimmed/
rm -rf ./results/03_pipeline_runs/*/human_genomics_pipeline/results/mapped/*_recalibrated_chrs.txt
rm -rf ./results/03_pipeline_runs/*/human_genomics_pipeline/results/qc/fastqc/
rm -rf ./results/03_pipeline_runs/*/human_genomics_pipeline/results/qc/multiqc_data/
rm -rf ./results/03_pipeline_runs/*/vcf_annotation_pipeline/results/annotated/*.txt
rm -rf ./results/03_pipeline_runs/*/human_genomics_pipeline/.git
rm -rf ./results/03_pipeline_runs/*/vcf_annotation_pipeline/git
rm -rf ./results/03_pipeline_runs/cohort/vcf_annotation_pipeline/
rm -rf ./results/03_pipeline_runs/cohort/human_genomics_pipeline/results/called/
rm -rf ./results/03_pipeline_runs/singleton/human_genomics_pipeline/results/called/
rm -rf ./results/03_pipeline_runs/cohort/pedigrees/

rm -rf ./results/04_manual_annotation/singleton/22CG019_raw_snps_indels*
rm -rf ./results/04_manual_annotation/cohort/21CG0001_filtered_dbnsfp_vep_cadd_dbsnp_posteriors_denovo.multiallelicsites.vcf*

Backup project

rsync -av /NGS/humangenomics/active/2022/run/hyperparathyroid_analysis_20221102/ /NGS/clinicalgenomics/archive/2022/results/hyperparathyroid_analysis_20221102/