#!/usr/bin/env bash
set -euo pipefail

GENOME=mm10
OUTROOT=HOMER_LESS
PREPARSED_DIR="$(pwd)/preparsed"
mkdir -p "$OUTROOT" "$PREPARSED_DIR"

MAX_JOBS=4
PTHREAD=4

job_count=0
for f in *RUVr_k3_filter.txt; do
  [ -e "$f" ] || continue

  base="${f%.txt}"
  outdir="${OUTROOT}/${base}"
  mkdir -p "$outdir"

  echo "Running $f -> $outdir"
  findMotifsGenome.pl "$f" "$GENOME" "$outdir" \
    -size given -p "$PTHREAD" -preparsedDir "$PREPARSED_DIR" \
    > "${outdir}/homer.stdout.log" 2> "${outdir}/homer.stderr.log" &

  ((job_count+=1))
  if (( job_count % MAX_JOBS == 0 )); then
    wait
  fi
done

wait
echo "All done. Results in: $OUTROOT/"