60 lines
1.7 KiB
Bash
60 lines
1.7 KiB
Bash
#!/usr/bin/env bash
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# Usage: ./run_evaluation_dmel.sh pathto/outputdir
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# See the isONcorrect paper https://www.nature.com/articles/s41467-020-20340-8 where this dataset is described
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if [[ "$#" -lt 1 ]]; then
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echo "usage: run_evaluation_dmel.sh <outdir> [nextflow.config]"
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exit 1
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fi
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if [[ "$#" -eq 1 ]]; then
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config=''
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fi
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if [[ "$#" -eq 2 ]]; then
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config="-c $2";
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fi
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OUTDIR=$1;
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FASTQ_URL="http://ftp.sra.ebi.ac.uk/vol1/fastq/ERR358/005/ERR3588905/ERR3588905_1.fastq.gz"
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REF_URL="http://ftp.ensembl.org/pub/release-99/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna.toplevel.fa.gz"
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GFF_URL="http://ftp.ensembl.org/pub/release-99/gff3/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.28.99.gff3.gz"
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DATA_DIR="$OUTDIR/data"
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READS_DIR="$DATA_DIR/reads"
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FASTQ="$READS_DIR/ERR3588905_1.fastq.gz"
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REF="$DATA_DIR/Drosophila_melanogaster.BDGP6.28.dna.toplevel.fa"
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GFF="$DATA_DIR/Drosophila_melanogaster.BDGP6.28.99.gff3"
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mkdir -p $READS_DIR
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if [ ! -f $REF ];
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then (echo "downloading reference genome"; cd $DATA_DIR; curl -L -C - -O $REF_URL); gzip -d ${REF}.gz
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fi
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if [ ! -f $GFF ];
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then
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(echo "downloading reference annotation"; cd $DATA_DIR; curl -L -C - -O $GFF_URL); gzip -d ${GFF}.gz
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fi
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if [ ! -f $FASTQ ];
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then (echo "downloading reads"; cd $READS_DIR; curl -L -C - -O $FASTQ_URL); gzip -d ${FASTQ}.gz
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fi
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OUT_REF="$OUTDIR/ref"
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OUT_DENOVO="$OUTDIR/denovo"
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nextflow run ../ --fastq $READS_DIR $config \
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--ref_genome $REF --ref_annotation $GFF -profile local --out_dir $OUT_REF --minimap2_opts '-uf --splice-flank=no' \
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-w $OUT_REF/workspace -resume;
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echo "Doing de novo evaluation"
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nextflow run ../ --fastq $READS_DIR $config --denovo -profile local --out_dir $OUT_DENOVO \
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-w $OUT_DENOVO/workspace -resume;
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