diff --git a/target/nextflow/mapping_and_qc/.config.vsh.yaml b/target/nextflow/mapping_and_qc/.config.vsh.yaml index 4c715c1..ef29179 100644 --- a/target/nextflow/mapping_and_qc/.config.vsh.yaml +++ b/target/nextflow/mapping_and_qc/.config.vsh.yaml @@ -162,7 +162,7 @@ build_info: output: "target/nextflow/mapping_and_qc" executable: "target/nextflow/mapping_and_qc/main.nf" viash_version: "0.9.0-RC6" - git_commit: "861319f5ddc22d51899493bcd30e7066c42193cb" + git_commit: "d87d344d4e46dc6f938e57a009607946ed31447c" git_remote: "https://github.com/viash-hub/playground" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/cutadapt" diff --git a/target/nextflow/mapping_and_qc/main.nf b/target/nextflow/mapping_and_qc/main.nf index 614b891..2602439 100644 --- a/target/nextflow/mapping_and_qc/main.nf +++ b/target/nextflow/mapping_and_qc/main.nf @@ -2989,7 +2989,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/mapping_and_qc", "viash_version" : "0.9.0-RC6", - "git_commit" : "861319f5ddc22d51899493bcd30e7066c42193cb", + "git_commit" : "d87d344d4e46dc6f938e57a009607946ed31447c", "git_remote" : "https://github.com/viash-hub/playground" }, "package_config" : { diff --git a/test_data.sh b/test_data.sh index c96feca..52faa90 100755 --- a/test_data.sh +++ b/test_data.sh @@ -51,12 +51,12 @@ sed -i -e 's/^.*chromosome=\(.*\)\]$/>chr\1/' "$TEST_DATA_DIR/S288C_reference_ge 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 "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff" \ - --sjdbGTFtagExonParentTranscript Parent \ - --sjdbOverhang 100 \ + --genome_fasta_files "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa" \ + --sjdb_gtf_file "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff" \ + --sjdb_gtf_tag_exon_parent_transcript Parent \ + --sjdb_overhang 100 \ --publish_dir "$TEST_DATA_DIR" \ - --sjdbGTFfeatureExon noncoding_exon \ + --sjdb_gtf_feature_exon noncoding_exon \ --index S288C_reference_genome_Current_Release_STAR fi