CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
62 lines
2.0 KiB
Bash
Executable File
62 lines
2.0 KiB
Bash
Executable File
#!/bin/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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# settings
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ID=reference_gencodev41_chr1
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OUT=resources_test/$ID
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mkdir -p "$OUT"
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wget "https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip" -O "$OUT/ERCC92.zip"
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# Download JASPAR files for reference building
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# Source of the code below: https://support.10xgenomics.com/single-cell-atac/software/release-notes/references#GRCh38-2020-A-2.0.0
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motifs_url="https://jaspar.elixir.no/download/data/2024/CORE/JASPAR2024_CORE_non-redundant_pfms_jaspar.txt"
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motifs_in="${OUT}/JASPAR2024_CORE_non-redundant_pfms_jaspar.txt"
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if [ ! -f "$motifs_in" ]; then
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curl -sS "$motifs_url" > "$motifs_in"
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fi
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# Change motif headers so the human-readable motif name precedes the motif
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# identifier. So ">MA0004.1 Arnt" -> ">Arnt_MA0004.1".
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motifs_modified="${OUT}/$(basename "$motifs_in").modified"
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awk '{
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if ( substr($1, 1, 1) == ">" ) {
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print ">" $2 "_" substr($1,2)
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} else {
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print
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}
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}' "$motifs_in" > "$motifs_modified"
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cat > /tmp/params.yaml << HERE
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param_list:
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- id: "$ID"
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genome_fasta: "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz"
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transcriptome_gtf: "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz"
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target: ["bd_rhapsody", "cellranger_arc"]
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output_fasta: "reference.fa.gz"
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output_gtf: "reference.gtf.gz"
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non_nuclear_contigs: null
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output_cellranger_arc: "reference_cellranger.tar.gz"
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output_bd_rhapsody: "reference_bd_rhapsody.tar.gz"
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bdrhap_extra_star_params: "--genomeSAindexNbases 12 --genomeSAsparseD 2"
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motifs_file: "$motifs_modified"
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subset_regex: "chr1"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/workflows/ingestion/make_reference/main.nf \
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-profile docker \
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-c ./src/workflows/utils/labels_ci.config \
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-params-file /tmp/params.yaml \
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--publish_dir $OUT \
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-resume
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