CI
a518d2ead8
Build pipeline: viash-hub.biobox.main-v9whr
Source commit: 5f6516e9c0
Source message: Bump viash version (#172)
* bump viash version
* fix agat requirements
30 lines
1.6 KiB
Bash
30 lines
1.6 KiB
Bash
#!/bin/bash
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set -e
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## VIASH START
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## VIASH END
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mkdir -p $par_index
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STAR \
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--runMode genomeGenerate \
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--genomeDir $par_index \
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--genomeFastaFiles $par_genome_fasta_files \
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${meta_cpus:+--runThreadN "${meta_cpus}"} \
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${par_sjdb_gtf_file:+--sjdbGTFfile "${par_sjdb_gtf_file}"} \
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${par_sjdbOverhang:+--sjdbOverhang "${par_sjdbOverhang}"} \
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${par_genome_sa_index_nbases:+--genomeSAindexNbases "${par_genome_sa_index_nbases}"} \
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${par_sjdb_gtf_chr_prefix:+--sjdbGTFchrPrefix "${par_sjdb_gtf_chr_prefix}"} \
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${par_sjdb_gtf_feature_exon:+--sjdbGTFfeatureExon "${par_sjdb_gtf_feature_exon}"} \
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${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtagExonParentTranscript "${par_sjdb_gtf_tag_exon_parent_transcript}"} \
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${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtagExonParentGene "${par_sjdb_gtf_tag_exon_parent_gene}"} \
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${sjdb_gtf_tag_exon_parent_gene_name:+--sjdbGTFtagExonParentGeneName "${sjdb_gtf_tag_exon_parent_gene_name}"} \
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${sjdb_gtf_tag_exon_parent_gene_type:+--sjdbGTFtagExonParentGeneType "${sjdb_gtf_tag_exon_parent_gene_type}"} \
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${par_limit_genome_generate_ram:+--limitGenomeGenerateRAM "${par_limit_genome_generate_ram}"} \
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${par_genome_chr_bin_nbits:+--genomeChrBinNbits "${par_genome_chr_bin_nbits}"} \
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${par_genome_sa_sparse_d:+--genomeSAsparseD "${par_genome_sa_sparse_d}"} \
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${par_genome_suffix_length_max:+--genomeSuffixLengthMax "${par_genome_suffix_length_max}"} \
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${par_genome_transform_type:+--genomeTransformType "${par_genome_transform_type}"} \
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${par_genome_transform_vcf:+--genomeTransformVCF "${par_genome_transform_vCF}"} \
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