Script_for_denovo_s3

#!/bin/bash

#This is used in my Docker container

##PATH
#DRAP install directory in the Docker container
cd /usr/local/src/drap

#DRAP configuration PATH
cd /usr/local/src/drap/cfg

#Edit configuration (change "local_cpu" and "n_cpu")
vi /usr/local/src/drap/cfg/drap.cfg

#Trimmed and filtered by Kraken2 sequence PATH
cd /mnt/data/pri_data/kraken

##Step 1: merge samples from brain and skin(R) separately, forward and reverse reads (1 and 2).
cd /mnt/data/pri_data/kraken && pwd && ls
# Merge all uf*B_1.fq.gz into one compressed file
cat uf*B_1.fq.gz > merged_B_1.fq.gz

# Merge all uf*B_2.fq.gz into one compressed file
cat uf*B_2.fq.gz > merged_B_2.fq.gz

# Merge all uf*R_1.fq.gz into one compressed file
cat uf*R_1.fq.gz > merged_R_1.fq.gz

# Merge all uf*R_2.fq.gz into one compressed file
cat uf*R_2.fq.gz > merged_R_2.fq.gz


##Step 2: run DRAP for denovo assembly
cd /usr/local/src/drap && pwd && ls

###ONLY DO THIS IF YOU RUN THIS FOR THE FIRST TIME###
#Edit the CPU number used in tgicl (It always fails when more than 6 CPUs are used here). This is a tool used in step 5. 
vi /usr/local/src/drap/bin/runAssembly.sh

# Change the second line into the following command
tgicl all_dbg.fa -c 6 -l 60 -p 96 -s 100000
###


#######auto_drap.sh######
#####Following script can be saved as a shell script to let it run automatically (to better arrange time)###
#!/bin/bash
set -euo pipefail

# Function to run a command and check for errors
run_step() {
    local step_name="$1"
    shift
    echo "=== Starting: $step_name ==="
    if "$@"; then
        echo "=== $step_name completed successfully ==="
    else
        echo "!!! ERROR: $step_name failed. Stopping pipeline. !!!"
        exit 1
    fi
}

# Step 1: runDrap for brain samples
run_step "runDrap (brain)" \
runDrap \
  --outdir /mnt/data/out_drap_s3_b \
  --R1 /mnt/data/pri_data/kraken/merged_B_1.fq.gz \
  --R2 /mnt/data/pri_data/kraken/merged_B_2.fq.gz \
  --dbg trinity \
  --no-trim \
  --norm-mem 200 \
  --dbg-mem 200 \
  --discardN \
  --coverage 0,0.5,1 \
  --no-rate

# Step 2: runDrap for skin samples
run_step "runDrap (skin)" \
runDrap \
  --outdir /mnt/data/out_drap_s3_r \
  --R1 /mnt/data/pri_data/kraken/merged_R_1.fq.gz \
  --R2 /mnt/data/pri_data/kraken/merged_R_2.fq.gz \
  --dbg trinity \
  --no-trim \
  --norm-mem 200 \
  --dbg-mem 200 \
  --discardN \
  --coverage 0,0.5,1 \
  --no-rate

# Step 3: runMeta to merge both assemblies, remember to add "--no-rate", or it will take longer...
run_step "runMeta (merge brain + skin)" \
runMeta \
  --drap-dirs /mnt/data/out_drap_s3_b,/mnt/data/out_drap_s3_r \
  --outdir /mnt/data/meta_s3 \
  --coverage 0,0.5,1 \
  --no-rate

echo "=== All steps completed successfully! ==="
############