Bioinformatics-and-Server-Extras/workflow_single_library_assemblies_eb.sh at master · ToBoDev/Bioinformatics-and-Server-Extras · GitHub

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#!/bin/bash

#set genome as eukaryote or prokaryote
G_size="EUK"
#G_size="PRO"

#define desired total number of cores to use
NUMPROC=48
#define max memory (in GB) to use
MEMORY=350
#define number of 'splits' for large jobs - for small genome assembly, you can split resources to save time
if [ $G_size = 'EUK' ]; then SPLITSa=1; fi
if [ $G_size = 'PRO' ]; then SPLITSa=3; fi

#set project path
PROJ=${PWD##*/}
#USR_KMER="71,81,91,99,121,127"

#suggested file structure
# project
# |____raw
# |   |____genome1
# |   |____genome2
# |   |____genome3
# |   |____...
# |____fastqc
# |____assembly
# |____quast
# |____etc
# |____...
#ddefine resources to use

#Trim galore:
#trim adapter seqs, overrep seqs, qual < 20 (also dedup w/ erika's suggestion?)
if [ ! -d "trimming" ]; then mkdir trimming; fi
if [ ! -d "assembly" ]; then mkdir assembly; fi
if [ ! -d "quast" ]; then mkdir quast; fi

#####TRIMMING#####-----------------------------------------------------------
if test -n "$(find ./raw -name '*R2*' -print -quit)"; then
    parallel -j $NUMPROC trim_galore --paired --illumina --fastqc -o trimming/ ::: ` find  ./raw  -name "*_R1*.f*.gz" | sort ` :::+ ` find  ./raw  -name "*_R2*.f*.gz" | sort `
    #FWDS=`find ./trimming -name "*R1*.gz" | sort | uniq`
    #REVS=(` find ./trimming -name "*R2*.gz" | sort | uniq `)
else
   parallel -j $NUMPROC trim_galore --illumina --fastqc -o trimming/ ::: ` find  ./raw  -name "*_R1*.f*.gz" `
   FWDS=`find ./trimming -name "*val_1*.gz" | sort | uniq`
fi

#####SPADES ASSEMBLY#####
if test -n "$(find ./raw -name '*R2*' -print -quit)"; then
    echo reverse reads found. proceeding with paired end assembly using $NUMPROC cores and $MEMORY GB memory
    parallel -j $SPLITSa spades.py --careful -1 {1} -2 {2} -t $(( $NUMPROC / $SPLITSa )) -m $(( $MEMORY / $SPLITSa )) -o ./assembly/{3}_default_kmer ::: \
    ` find ./trimming -name "*val_1*.gz" | sort | uniq ` :::+ \
    ` find ./trimming -name "*val_2*.gz" | sort | uniq ` :::+ \
    ` find ./trimming -name "*val_1*.gz" | sort | uniq | cut -d "/" -f3 | cut -d "_" -f1 `
else
    echo no reverse reads found. proceeding with single end assebmly using $NUMPROC cores and $MEMORY GB memory
    parallel -j $SPLITSa spades.py --careful -1 {1} -t $(( $NUMPROC / $SPLITSa )) -m $(( $MEMORY / $SPLITSa )) -o ./assembly/{3}_default_kmer ::: \
    ` find ./trimming -name "*val_1*.gz" | sort | uniq ` :::+ \
    ` find ./trimming -name "*val_1*.gz" | sort | uniq | cut -d "/" -f3 | cut -d "_" -f1 `
fi

#####QUAST#####-----------------------------------------------------------
#per KMER
# for genome in `find ./assembly -maxdepth 1 -name "*kmer" -type d | cut -d "/" -f3`; do
#     KMERS=(` find ./assembly/$genome/ -maxdepth 1 -name "K*" | cut -d "/" -f4 | sort | uniq `)
#     cp ./assembly/${genome}/contigs.fasta ./quast/"${genome}_contigs.fasta"
#          for KMER in `find ./assembly/$genome/ -maxdepth 1 -name "K*" | cut -d "/" -f4 | sort | uniq`; do
#              cp ./assembly/${genome}/${KMER}/final_contigs.fasta ./quast/${genome}_${KMER}.fasta
#         done
#     by_kmer=("${KMERS[@]/#/./quast/${genome}_}")
#     by_kmer_files=("${by_kmer[@]/%/.fasta}")
#     quast.py -e -t $NUMPROC -m $MEMORY ./quast/${genome}_contigs.fasta "${by_kmer_files[@]}" -o ./quast/${genome}_results/
# done

#all default KMER selection
#all_user=(` find ./quast/*usr*contigs.fasta  -type f `)
#quast.py -e -t $NUMPROC -m $MEMORY  "${all_user[@]}" -o ./quast/usr_spades/

#spades default settings
#all default KMER selection

#copy over contig outputs for
parallel -j $NUMPROC cp ./assembly/{}/contigs.fasta ./quast/{}_contigs.fasta ::: \
` find ./assembly -maxdepth 1 -type d | sort | uniq | cut -d "/" -f3 `

all_default=(` find ./quast/*contigs.fasta  -type f `)

if [ $G_size = "EUK" ]; then
    quast.py --large -e -k -t $NUMPROC -m $MEMORY "${all_default[@]}" -o ./quast/default_spades/  ; fi

if [ $G_size = "PRO" ]; then
    quast.py --gene-finding -b -t $NUMPROC -m $MEMORY "${all_default[@]}" -o ./quast/default_spades/  ; fi

#########STOP######-----------------------------------------------------------
#before proceeding: evaluate your quast results. Choose desired de novo, copy to ./assemly with a name to include *chosen.fasta