TR-Benchmarking

Tandem repeat benchmarking project.

Run Nextflow

Submit the job with:

sbatch -J tr_bench   -p amilan --qos=normal   --time=08:00:00 --mem=2G   --output=logs/%x_%j.out --error=logs/%x_%j.err   --wrap="bash run_benchmarking_slurm.sh run_benchmarking.nf --list ont_bam.list --ref /pl/active/dashnowlab/data/ref-genomes/human_GRCh38_no_alt_analysis_set.fasta"

What it does

• -J tr_bench — sets the Slurm job name.
• -p amilan --qos=normal — selects the partition and QoS.
• --time=08:00:00 --mem=2G — walltime and memory request.
• --output/--error — logs saved to logs/ with job id.
• --wrap="bash …" — runs the wrapper that launches Nextflow:
  • run_benchmarking_slurm.sh invokes run_benchmarking.nf
  • --list ont_bam.list points to your input list (one BAM/CRAM per line)
  • --ref ...fasta provides the GRCh38 reference path

Separate Shell Scripts

Run_Atarva

cd /pl/active/dashnowlab/projects/TR-benchmarking/

while IFS=$'\t' read -r CRAM KARYOTYPE; do
  [[ -z "$CRAM" || "$CRAM" =~ ^[[:space:]]*# ]] && continue
  SAMPLE="$(basename "$CRAM" .haplotagged.cram)"
  SAMPLE="${SAMPLE%.cram}"
  sbatch -J "atarva_${SAMPLE}" run_atarva.sh "$CRAM" "$KARYOTYPE"
done < test_bam.list

Run LongTR

cd /pl/active/dashnowlab/projects/TR-benchmarking/

while IFS=$'\t' read -r CRAM KARYOTYPE; do
  [[ -z "$CRAM" || "$CRAM" =~ ^[[:space:]]*# ]] && continue
  SAMPLE="$(basename "$CRAM" .haplotagged.cram)"
  SAMPLE="${SAMPLE%.cram}"
  sbatch -J "longtr_${SAMPLE}" run_longtr.sh "$CRAM" "$KARYOTYPE"
done < test_bam.list

Run Straglr

cd /pl/active/dashnowlab/projects/TR-benchmarking/

while IFS=$'\t' read -r CRAM KARYOTYPE; do
  [[ -z "$CRAM" || "$CRAM" =~ ^[[:space:]]*# ]] && continue
  SAMPLE="$(basename "$CRAM" .haplotagged.cram)"
  SAMPLE="${SAMPLE%.cram}"
  sbatch -J "straglr_${SAMPLE}" run_straglr.sh "$CRAM" "$KARYOTYPE"
done < test_bam.list

Run TRSV

cd /pl/active/dashnowlab/projects/TR-benchmarking/

while IFS=$'\t' read -r CRAM KARYOTYPE; do
  [[ -z "$CRAM" || "$CRAM" =~ ^[[:space:]]*# ]] && continue
  SAMPLE="$(basename "$CRAM" .haplotagged.cram)"
  SAMPLE="${SAMPLE%.cram}"
  sbatch -J "trsv_${SAMPLE}" run_trsv.sh "$CRAM" "$KARYOTYPE"
done < test_bam.list