oncompnet.sh

#!/bin/bash

set -e 

# Quoted need to be parametrized
# Loop through multiple datasets
# Pass output to rmarkdown and generate pdf
# Document

printToLog() {
	date +"%F__%T ---> $1"
}

usage () {
  printf "USAGE:\n"
  printf "`basename $0` <analysis-name> <input-bam-file> <cancer_acronym> <nThreads> <input-hotspots-bed-file (optional)>\n\n"
}

exitWithError () {
  printf "\n***ERROR: $1\n\n"
  usage
  exit
}

if [[ $# == 4 ]]; then
    WORKFLOW="local_workflow.sh"
elif [[ $# == 5 ]]; then
    WORKFLOW="local_workflow_hotspots.sh"
else
    exitWithError "Wrong number of parameters."
fi

export ANALYSIS_NAME="$1"
export INPUT_BAM_name="$2"
export CANCER="$3"
export THREADS="$4"
export HOTSPOTS_BED_name="$5"

export MOUNT_DIR="/data"
export LOCAL_DIR="/media/galadriel/fleming/oncopmnet/oncopmnet_pipeline"
export HGREF="$MOUNT_DIR/ref_genome/hg19/hg19.fasta"
export PARAMS_FILE="$MOUNT_DIR/params/gsfak.json"
export TARGETS_BED="$MOUNT_DIR/bed/solid_custom_merged.bed"
export INPUT_BAM="$MOUNT_DIR/datasets/$ANALYSIS_NAME/$INPUT_BAM_name"
export HOTSPOTS_BED="$MOUNT_DIR/hotspots/$HOTSPOTS_BED_name"

export PREFIX=Sample_${INPUT_BAM_name%".bam"}
export MOUNT_OUTDIR="$MOUNT_DIR/tvc-out/$ANALYSIS_NAME/$PREFIX"
export LOCAL_OUTDIR="$LOCAL_DIR/tvc-out/$ANALYSIS_NAME/$PREFIX"
export VCF_OUT="$LOCAL_OUTDIR"/TSVC_variants.vcf
export NORM_VCF_OUT="$LOCAL_OUTDIR"/TSVC_variants_norm.vcf

mkdir -p "$LOCAL_OUTDIR/logs"

printToLog "Statring variant calling analysis with TVC in temporary container:n"
printToLog "DOCKER RUN START" > $LOCAL_OUTDIR/logs/out 2>$LOCAL_OUTDIR/logs/error
# --name Anlysis specific name or ID
# -d detached mode, runs container in the background
# -t allocate a pseudo tty
# -v mounts the volume "oncopmnet_pipeline" into container's "$MOUNT_DIR" directory
docker run \
--name tmp_"$ANALYSIS_NAME"_"$INPUT_BAM_name" \
-d \
-t \
-v /media/galadriel/fleming/oncopmnet/oncopmnet_pipeline:"$MOUNT_DIR" sgsfak/tmap-tvc

printToLog "Running TVC analysis in containter's mounted directory"
printToLog "DOCKER EXEC START">> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error
# -e env variables passed into the container
docker exec \
-e PREFIX \
-e HGREF \
-e PARAMS_FILE \
-e TARGETS_BED \
-e HOTSPOTS_BED \
-e INPUT_BAM_name \
-e ANALYSIS_NAME \
-e INPUT_BAM \
-e MOUNT_OUTDIR \
-e THREADS \
-it tmp_"$ANALYSIS_NAME"_"$INPUT_BAM_name" "$MOUNT_DIR"/scripts/"$WORKFLOW" >> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error

printToLog "Stopping temporary docker container:"
docker stop tmp_"$ANALYSIS_NAME"_"$INPUT_BAM_name"
printToLog "Removing temporary docker container:"
docker rm tmp_"$ANALYSIS_NAME"_"$INPUT_BAM_name"

# Normalize - Break multiallelic variants with BCFtools (-norm)
printToLog "Normalizing vcf and breaking multiallelic variants"
printToLog "BCFTOOLS NOTMALISATION START">> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error
"$LOCAL_DIR"/tools/bcftools-1.10.2/bcftools norm \
-f "$LOCAL_DIR"/ref_genome/hg19/hg19.fasta \
-m- "$VCF_OUT" \
-o "$NORM_VCF_OUT" >> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error

# Annotate VCF with Bioconductor's VariantAnnotation
printToLog "Running variant annotaion with VariantAnnotation package"
printToLog "VARIANTANNOTATION START">> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error
Rscript -e "sampleName = '$PREFIX'; cancer = '$CANCER'; vcfDir = '$NORM_VCF_OUT'; output = '$LOCAL_OUTDIR'; rmarkdown::render('scripts/oncopmnet.Rmd', output_file = 'oncopmnet_report.html', output_dir = output)" >> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error

printToLog "Printing PDF"
printToLog "WEASYPRINT START">> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error
python3 -m weasyprint "$LOCAL_OUTDIR/oncopmnet_report.html" "$LOCAL_OUTDIR/oncopmnet_report.pdf" -s "report_extra/styles.css" >> $LOCAL_OUTDIR/logs/out 2>>$LOCAL_OUTDIR/logs/error

printToLog "Analysis Complete!"
printf "\nResults in $LOCAL_OUTDIR \n\n"