5b1018434e
Build pipeline: vsh-ci-template-8vdc6
Source commit: 861319f5dd
Source message: Merge pull request #4 from viash-hub/update-star-align-params
update param
75 lines
3.4 KiB
Bash
Executable File
75 lines
3.4 KiB
Bash
Executable File
#/usr/bin/env bash
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set -eo pipefail
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# ensure that the command below is run from the root of the repository
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REPO_ROOT=$(git rev-parse --show-toplevel)
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cd "$REPO_ROOT"
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TEST_DATA_DIR="test_data"
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mkdir -p "$TEST_DATA_DIR"
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if [ ! -f "$TEST_DATA_DIR/SRR1569895_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR1569895_2.fastq" ]; then
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docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1569895
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fi
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if [ ! -f "$TEST_DATA_DIR/SRR1570800_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR1570800_2.fastq" ]; then
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docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1570800
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fi
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head -n 10000 "$TEST_DATA_DIR/SRR1569895_1.fastq" > "$TEST_DATA_DIR/SRR1569895_1_subsample.fastq"
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head -n 10000 "$TEST_DATA_DIR/SRR1569895_2.fastq" > "$TEST_DATA_DIR/SRR1569895_2_subsample.fastq"
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head -n 10000 "$TEST_DATA_DIR/SRR1570800_1.fastq" > "$TEST_DATA_DIR/SRR1570800_1_subsample.fastq"
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head -n 10000 "$TEST_DATA_DIR/SRR1570800_2.fastq" > "$TEST_DATA_DIR/SRR1570800_2_subsample.fastq"
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export NXF_SCM_FILE="$TEST_DATA_DIR/scm.config"
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cat > $NXF_SCM_FILE << EOF
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providers {
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vsh {
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platform = 'gitlab'
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server = 'https://viash-hub.com/'
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}
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}
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EOF
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if [ ! -f "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz" ]; then
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wget http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_Current_Release.tgz \
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-O "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz"
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fi
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if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release" ]; then
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nextflow run vsh/craftbox -hub vsh -r main -main-script target/nextflow/untar/main.nf \
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-profile docker \
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--input "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz" \
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--output "S288C_reference_genome_Current_Release" \
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--publish_dir "$TEST_DATA_DIR"
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fi
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gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
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gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
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sed -i -e 's/^.*chromosome=\(.*\)\]$/>chr\1/' "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
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if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR" ]; then
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nextflow run vsh/biobox -hub vsh -r main -main-script target/nextflow/star/star_genome_generate/main.nf \
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-profile docker \
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--genomeFastaFiles "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa" \
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--sjdbGTFfile "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff" \
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--sjdbGTFtagExonParentTranscript Parent \
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--sjdbOverhang 100 \
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--publish_dir "$TEST_DATA_DIR" \
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--sjdbGTFfeatureExon noncoding_exon \
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--index S288C_reference_genome_Current_Release_STAR
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fi
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PARAMS_FILE=params_file.yaml
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cat > $PARAMS_FILE << EOF
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param_list:
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- id: SRR1569895
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input_r1: $TEST_DATA_DIR/SRR1569895_1_subsample.fastq
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input_r2: $TEST_DATA_DIR/SRR1569895_2_subsample.fastq
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- id: SRR1570800
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input_r1: $TEST_DATA_DIR/SRR1570800_1_subsample.fastq
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input_r2: $TEST_DATA_DIR/SRR1570800_2_subsample.fastq
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publish_dir: foo
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reference: $TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR
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EOF
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