SPAdes.sh

#!/bin/bash

#Assemble contigs using SPAdes
#Run in the conda environmet

#!/usr/bin/env bash

#tell bash where to find conda
export MYCONDAPATH=/home/bsalehe/miniconda3

#activate spades env
source ${MYCONDAPATH}/bin/activate spades

Usage="SPAdes.sh <F_read.fa> <R_read.fa> <output_directory> <correct/only-assembler> [<coverage_cutoff>]"
echo "$Usage"

R1="$1"
R2="$2"
OutDir="$3"
#Correction=$4
Cutoff="off"

sname=$(basename $R1 _L001_R1_trimmed.fastq.gz)

## check the spades cutoff in the command
if [ $5 ]; then
	Cutoff=$5
fi

CurPath=$PWD 
WorkDir=$TMPDIR/${SLURM_JOB_USER}_${SLURM_JOBID}

mkdir -p $WorkDir

F_Read=$(basename $R1)
R_Read=$(basename $R2)

cp $CurPath/$R1 $WorkDir/$F_Read
cp $CurPath/$R2 $WorkDir/$R_Read


echo "Running SPADES with the following in='$R1 $R2' $OutDir "
#echo "You have set read correction to: $Correction"
echo "Coverage cutoff set to $Cutoff"

#if [[ "$Correction" == 'correct' ]]; then
#   spades.py -k 21,33,55,77,99,127 --phred-offset 33 --careful -1 $WorkDir/$F_Read -2 $WorkDir/$R_Read -o $WorkDir/. --cov-cutoff "$Cutoff"
#elif [[ "$Correction" == 'only-assembler' ]]; then
spades.py -k 21,33,55,77,99,127  --phred-offset 33 --careful -1 $WorkDir/$F_Read -2 $WorkDir/$R_Read -o $WorkDir/. --cov-cutoff "$Cutoff"
#else
#   echo "Please set fourth option - whether you require read correction [correct / only-assembler]"
#   exit
#fi

echo "Filtering contigs smaller than 500bp"
mkdir -p $WorkDir/filtered_contigs
FilterDir=/home/gomeza/git_repos/scripts/bioinformatics_tools/Assembly_qc
python2 $FilterDir/filter_contigs.py $WorkDir/contigs.fasta 500 > $WorkDir/filtered_contigs/contigs_min_500bp.fasta

rm $WorkDir/$F_Read
rm $WorkDir/$R_Read
mkdir -p $CurPath/$OutDir
cp -r $WorkDir/* $CurPath/$OutDir/.
echo "files copied"

#deactivate spades
conda deactivate