Build branch main with version main (173327cc)

Build pipeline: vsh-ci-build-template-k4qzr

Source commit: 173327cc56

Source message: Cellranger multi conversion: fix combined AB + CB probe experiments (#1062)

resources_test_scripts/ref_gencodev41_chr1.sh

@@ -0,0 +1,61 @@
+#!/bin/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"
+
+# settings
+ID=reference_gencodev41_chr1
+OUT=resources_test/$ID
+
+mkdir -p "$OUT" 
+
+wget "https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip" -O "$OUT/ERCC92.zip"
+
+# Download JASPAR files for reference building
+# Source of the code below: https://support.10xgenomics.com/single-cell-atac/software/release-notes/references#GRCh38-2020-A-2.0.0
+motifs_url="https://jaspar.elixir.no/download/data/2024/CORE/JASPAR2024_CORE_non-redundant_pfms_jaspar.txt"
+motifs_in="${OUT}/JASPAR2024_CORE_non-redundant_pfms_jaspar.txt"
+
+if [ ! -f "$motifs_in" ]; then
+    curl -sS "$motifs_url" > "$motifs_in"
+fi
+
+# Change motif headers so the human-readable motif name precedes the motif
+# identifier. So ">MA0004.1    Arnt" -> ">Arnt_MA0004.1".
+motifs_modified="${OUT}/$(basename "$motifs_in").modified"
+awk '{
+    if ( substr($1, 1, 1) == ">" ) {
+        print ">" $2 "_" substr($1,2)
+    } else {
+        print
+    }
+}' "$motifs_in" > "$motifs_modified"
+
+
+cat > /tmp/params.yaml << HERE
+param_list:
+  - id: "$ID"
+    genome_fasta: "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz"
+    transcriptome_gtf: "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz"
+    target: ["bd_rhapsody", "cellranger_arc"] 
+    output_fasta: "reference.fa.gz"
+    output_gtf: "reference.gtf.gz"
+    non_nuclear_contigs: null
+    output_cellranger_arc: "reference_cellranger.tar.gz"
+    output_bd_rhapsody: "reference_bd_rhapsody.tar.gz"
+    bdrhap_extra_star_params: "--genomeSAindexNbases 12 --genomeSAsparseD 2"
+    motifs_file: "$motifs_modified"
+    subset_regex: "chr1"
+HERE
+
+nextflow \
+  run . \
+  -main-script target/nextflow/workflows/ingestion/make_reference/main.nf \
+  -profile docker \
+  -c ./src/workflows/utils/labels_ci.config \
+  -params-file /tmp/params.yaml \
+  --publish_dir $OUT \
+  -resume