41 lines
1.2 KiB
Bash
Executable File
41 lines
1.2 KiB
Bash
Executable File
#!/bin/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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OUTDIR=$1;
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FASTQ_URL="http://ftp.sra.ebi.ac.uk/vol1/fastq/ERR358/005/ERR3588905/ERR3588905_1.fastq.gz"
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REF_URL="http://ftp.ensembl.org/pub/release-99/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna.toplevel.fa.gz"
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GFF_URL="http://ftp.ensembl.org/pub/release-99/gff3/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.28.99.gff3.gz"
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RESULTS_DIR="$OUTDIR/results"
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DATA_DIR="$OUTDIR/data"
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READS_DIR="$DATA_DIR/reads"
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FASTQ="$READS_DIR/ERR3588905_1.fastq"
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REF="$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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echo $READS_DIR;
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rm -fr $OUT_DIR/results
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mkdir -p $OUTDIR/data
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if [ ! -f $REF ];
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then (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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(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 (cd $READS_DIR; curl -L -C - -O $FASTQ_URL); gzip -d ${FASTQ}.gz
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fi
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nextflow run ../wf-isoforms --fastq $READS_DIR \
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--reference_genome $REF --annotation $GFF -profile conda --out_dir $OUTDIR \
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-w $OUTDIR/workspace -resume
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