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Build branch main with version main (ec3c23e)

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Build pipeline: vsh-ci-template-v8q2j

Source commit: ec3c23e349

Source message: Update test data script
This commit is contained in:
CI
2024-06-28 12:02:37 +00:00
commit edccce830a
36 changed files with 36998 additions and 0 deletions
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test_data.sh Executable file
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#/usr/bin/env bash
set -eo pipefail
# ensure that the command below is run from the root of the repository
REPO_ROOT=$(git rev-parse --show-toplevel)
cd "$REPO_ROOT"
TEST_DATA_DIR="test_data"
mkdir -p "$TEST_DATA_DIR"
if [ ! -f "$TEST_DATA_DIR/SRR1569895_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR1569895_2.fastq" ]; then
docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1569895
fi
if [ ! -f "$TEST_DATA_DIR/SRR1570800_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR1570800_2.fastq" ]; then
docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1570800
fi
export NXF_SCM_FILE="$TEST_DATA_DIR/scm.config"
cat > $NXF_SCM_FILE << EOF
providers {
vsh {
platform = 'gitlab'
server = 'https://viash-hub.com/'
}
}
EOF
if [ ! -f "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz" ]; then
wget http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_Current_Release.tgz \
-O "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz"
fi
if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release" ]; then
nextflow run vsh/craftbox -hub vsh -r main -main-script target/nextflow/untar/main.nf \
-profile docker \
--input "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz" \
--output "S288C_reference_genome_Current_Release" \
--publish_dir "$TEST_DATA_DIR"
fi
zcat "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
zcat "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
sed -i -e 's/^.*chromosome=\(.*\)\]$/>chr\1/' "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR" ]; then
nextflow run vsh/biobox -hub vsh -r main -main-script target/nextflow/star/star_genome_generate/main.nf \
-profile docker \
--genomeFastaFiles "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa" \
--sjdbGTFfile "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff" \
--sjdbGTFtagExonParentTranscript Parent \
--sjdbOverhang 100 \
--publish_dir "$TEST_DATA_DIR" \
--sjdbGTFfeatureExon noncoding_exon \
--index S288C_reference_genome_Current_Release_STAR
fi
PARAMS_FILE=params_file.yaml
cat > $PARAMS_FILE << EOF
param_list:
- id: SRR1569895
input_r1: $TEST_DATA_DIR/SRR1569895_1.fastq
input_r2: $TEST_DATA_DIR/SRR1569895_2.fastq
- id: SRR1570800
input_r1: $TEST_DATA_DIR/SRR1570800_1.fastq
input_r2: $TEST_DATA_DIR/SRR1570800_2.fastq
publish_dir: foo
reference: $TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR
EOF