#!/bin/bash
#SBATCH --job-name=16S_v3-v4
#SBATCH --nodes=1
#SBATCH -c 24
#SBATCH --mem=500G  
#SBATCH -p sm                     
#SBATCH -o cheese_%j.out    
#SBATCH -e cheese_%j.err 

module load java/17.0.12
module load nextflow

# =============================
# 1. Definir rutas
# =============================
DATA_DIR="/home/igbi/investigadores/paul.fernandez/queso/cheese"
OUT_DIR="${DATA_DIR}/results_1_cheese"
LOG_DIR="/home/igbi/investigadores/paul.fernandez/ampliseq_logs"
PIPELINE_DIR="/home/igbi/investigadores/paul.fernandez/ampliseq"

mkdir -p "${OUT_DIR}" "${LOG_DIR}"

# =============================
# 2. Caché de Singularity
# =============================
export NXF_SINGULARITY_CACHEDIR="${OUT_DIR}/singularity_cachedir"
mkdir -p "$NXF_SINGULARITY_CACHEDIR"

# =============================
# 3. Ejecutar nf-core/ampliseq
# =============================
nextflow run "${PIPELINE_DIR}" \
  -profile singularity \
  --input_folder "${DATA_DIR}" \
  --extension '/*_R{1,2}_001.fastq.gz' \
  --FW_primer "CCTACGGGDGGCWGCAG" \
  --RV_primer "GACTACNVGGGTMTCTAATCC" \
--metadata "${DATA_DIR}/Metadata.tsv" \
  --outdir "${OUT_DIR}" \
  --picrust \
  --ancom \
  --ancombc \
  -resume