Flumina

#!/bin/bash

date

# Check if a configuration file was provided
if [ -z "$1" ]; then
  echo "Usage: $0 path_to_config_file needed."
  exit 1
fi

CONFIG_FILE="$1"

# Check if the configuration file exists
if [ ! -f "$CONFIG_FILE" ]; then
  echo "Error: Configuration file not found at $CONFIG_FILE"
  exit 1
fi

# Source the configuration file
source "$CONFIG_FILE"

echo "Configuration file successfully loaded"

mkdir "$OUTPUT_DIRECTORY"

echo "Beginning read organization ... "

Rscript Scripts/organizeReads.R "$CONFIG_FILE"

echo "Beginning reference creation ... "

#Sets custom snakemake parameters
if [ "$FORCE_UNLOCK" = "TRUE" ]; then
    NOLOCK="--nolock"
else
    NOLOCK=""
fi

if [ "$CLUSTER_JOBS" != "FALSE" ]; then
    CLUSTER="--cluster \"$CLUSTER_JOBS\""
else
    CLUSTER=""
fi

#Sets the snakefile to use when disabling IRMA
if [ "$DISABLE_IRMA" == "TRUE" ]; then
    IRMA_RUN="Scripts/snakefile_process_SNPs.smk"
else
    IRMA_RUN="Scripts/snakefile_process_IRMA_SNPs.smk"
fi

#Copies reference to output directory so snakefile can find it
cp "$REFERENCE_FILE" "$OUTPUT_DIRECTORY"/reference.fa

#Export variable to global env
export CLUSTER_JOBS

#Runs make the reference snakemake function
snakemake --snakefile Scripts/snakefile_make-reference.smk --directory "$OUTPUT_DIRECTORY" -j $THREADS $NOLOCK

#Runs SNV calling pipeline

echo "Beginning SNV calling pipeline ... "

if [ "$CLUSTER_JOBS" != "FALSE" ]; then
    snakemake --snakefile $IRMA_RUN --directory "$OUTPUT_DIRECTORY" -j $THREADS $NOLOCK --cluster "$CLUSTER_JOBS"
else
    snakemake --snakefile $IRMA_RUN --directory "$OUTPUT_DIRECTORY" -j $THREADS $NOLOCK
fi

#Organizes IRMA only when not disabled
if [ "$DISABLE_IRMA" == "FALSE" ]; then
    Rscript Scripts/organizeIRMA.R "$CONFIG_FILE"
fi

Rscript Scripts/convertVCFtoTable.R "$CONFIG_FILE"

Rscript Scripts/findAAChanges.R "$CONFIG_FILE"

Rscript Scripts/outputSummary.R "$CONFIG_FILE"


date
# End of file