CI
f6ea42ed13
Build pipeline: viash-hub.rnaseq.bugfix-czsqc
Source commit: 7687d774f2
Source message: Merge remote-tracking branch 'origin/main' into bugfix
106 lines
5.0 KiB
Bash
Executable File
106 lines
5.0 KiB
Bash
Executable File
#!/bin/bash
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CURR=`pwd`
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### Get input fastq files for the minimal test
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DEST_FASTQ="testData/minimal_test/input_fastq"
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mkdir -p $DEST_FASTQ
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cd $DEST_FASTQ
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echo "Fetching FastQ files..."
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357070_1.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357070_2.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357071_1.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357071_2.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357072_1.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357072_2.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357073_1.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357074_1.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357075_1.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357076_1.fastq.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357076_2.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357071_1.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357071_2.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357072_1.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357072_2.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357073_1.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357074_1.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357075_1.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357076_1.fastq.gz
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wget https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/GSE110004/SRR6357076_2.fastq.gz
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cd $CURR
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### Get reference files for the minimal test
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DEST_REF="testData/minimal_test/reference"
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mkdir -p $DEST_REF
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cd $DEST_REF
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echo "Fetching reference data..."
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genome.fasta
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta
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wget https://raw.githubusercontent.com/nf-core/rnaseq/3.12.0/assets/rrna-db-defaults.txt
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gff.gz
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/transcriptome.fasta
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/gfp.fa.gz
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/bbsplit_fasta_list.txt
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# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/hisat2.tar.gz
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/salmon.tar.gz
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wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/rsem.tar.gz
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cd $CURR
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NEWDEST1_REF="$CURR/testData/minimal_test/reference/rRNA"
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mkdir -p $NEWDEST1_REF
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cd $NEWDEST1_REF
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for LINE in `cat ../rrna-db-defaults.txt`
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do
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wget $LINE
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done
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cd $CURR
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find $NEWDEST1_REF -type f > $DEST_REF/rrna-db-defaults.txt
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NEWDEST2_REF="$CURR/testData/minimal_test/reference/bbsplit_fasta"
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mkdir -p $NEWDEST2_REF
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while IFS=, read -r -a line; do
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url="${line[1]}"
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name="$NEWDEST2_REF/${line[0]}.fa"
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wget $url -O "$name"
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line+=("$name")
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IFS=','
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echo "${line[*]}" >> "$NEWDEST2_REF/tmp.txt"
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done < "$DEST_REF/bbsplit_fasta_list.txt"
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cut -d',' -f1,3 "$NEWDEST2_REF/tmp.txt" > "$DEST_REF/bbsplit_fasta_list.txt"
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rm "$NEWDEST2_REF/tmp.txt"
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