star

#!/bin/bash

# module init required when running on non-OSG resources, and has to sourced
# before set -e as sometimes it exits non-0 when a module environment is
# already set up
. /cvmfs/oasis.opensciencegrid.org/osg/sw/module-init.sh

set -e

module load samtools/1.3.1
module load java/8u25

set -v
set -o pipefail

CONNECT_USER=$1
RUN_ID=$2
REF_PATH=$3
BASE_NAME=$4
PART=$5
COMMON_NAME=$6
LAYOUT=$7

unzip 2.5.2b.zip

if [ $LAYOUT = "paired" ] ; then


     java -Xmx512m \
          -jar trimmomatic-0.36.jar PE -threads 1 -phred33 \
          $BASE_NAME-forward-$COMMON_NAME $BASE_NAME-reverse-$COMMON_NAME \
          left_result.paired_trim.forward_$COMMON_NAME.fastq /dev/null \
          right_result.paired_trim.reverse_$COMMON_NAME.fastq /dev/null \
          ILLUMINACLIP:fasta_adapter.txt:2:40:15 LEADING:3 TRAILING:6 SLIDINGWINDOW:4:15 MINLEN:50 \
          2>&1 | tee $BASE_NAME-$COMMON_NAME-trimmomatic.txt

     # empty outputs?
     LEFT_SIZE=`ls -l left_result.paired_trim.forward_$COMMON_NAME.fastq | cut -d ' ' -f 5`
     RIGHT_SIZE=`ls -l right_result.paired_trim.reverse_$COMMON_NAME.fastq | cut -d ' ' -f 5`
     if [ $LEFT_SIZE -lt 50 -o $RIGHT_SIZE -lt 50 ]; then
         echo "Warning: trimmomatic output was 0 sequences"
         touch $BASE_NAME-$COMMON_NAME-accepted_hits.bam
         exit 0
     fi


     STAR-2.5.2b/bin/Linux_x86_64_static/STAR --genomeDir . --sjdbFileChrStartEnd ./*.Splice_Sites.txt --runThreadN 1 \
                                         --outSAMtype BAM SortedByCoordinate \
                                         --readFilesIn left_result.paired_trim.forward_$COMMON_NAME.fastq right_result.paired_trim.reverse_$COMMON_NAME.fastq  | tee $BASE_NAME-$COMMON_NAME-out.txt

elif [ $LAYOUT = "single" ] ; then


    java -Xmx512m \
         -jar trimmomatic-0.36.jar SE -threads 1 -phred33 \
         $BASE_NAME-forward-$COMMON_NAME  \
         left_result.paired_trim.forward_$COMMON_NAME.fastq \
         ILLUMINACLIP:fasta_adapter.txt:2:40:15 LEADING:3 TRAILING:6 SLIDINGWINDOW:4:15 MINLEN:50 \
         2>&1 | tee $BASE_NAME-$COMMON_NAME-trimmomatic.txt

    # empty outputs?
    LEFT_SIZE=`ls -l left_result.paired_trim.forward_$COMMON_NAME.fastq | cut -d ' ' -f 5`
    if [ $LEFT_SIZE -lt 50 ] ; then
        echo "Warning: trimmomatic output was 0 sequences"
        touch $BASE_NAME-$COMMON_NAME-accepted_hits.bam
        exit 0
    fi


    STAR-2.5.2b/bin/Linux_x86_64_static/STAR --genomeDir . --sjdbFileChrStartEnd ./*.Splice_Sites.txt --runThreadN 1 \
                                         --outSAMtype BAM SortedByCoordinate \
                                         --readFilesIn left_result.paired_trim.forward_$COMMON_NAME.fastq | tee $BASE_NAME-$COMMON_NAME-out.txt
fi

mv Aligned.sortedByCoord.out.bam $BASE_NAME-$COMMON_NAME-accepted_hits.bam

mv Log.final.out $BASE_NAME-$COMMON_NAME-Log.final.out