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Copy pathrun_test_macrophage_chr21_SE.sh
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executable file
·22 lines (22 loc) · 1.03 KB
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nextflow run main.nf\
-profile tartu_hpc\
--readPathsFile /gpfs/hpc/home/a72094/datasets/open_access/testdata/readPathsFile_macrophages_SE.tsv\
--singleEnd\
--reverse_stranded\
--hisat2_index /gpfs/hpc/home/a72094/annotations/eQTLCatalogue/v0.1/hisat2_index_v96/Homo_sapiens.GRCh38.dna.primary_assembly\
--aligner 'hisat2'\
--skip_qc\
--skip_skip_multiqc\
--run_tx_exp_quant\
--run_txrevise\
--run_splicing_exp_quant\
--run_exon_quant\
--run_mbv\
--mbv_vcf /gpfs/hpc/home/a72094/datasets/open_access/testdata/macrophage_test_data/Alasoo_2018_chr21_test_samples.vcf.gz\
--saveReference\
--saveTrimmed\
--saveAlignedIntermediates\
--gtf /gpfs/hpc/home/a72094/annotations/eQTLCatalogue/v0.1/gencode.v30.annotation.no_chr.gtf\
--fasta /gpfs/hpc/home/a72094/annotations/eQTLCatalogue/v0.1/Homo_sapiens.GRCh38.dna.primary_assembly.fa\
--txrevise_gffs '/gpfs/hpchome/a72094/annotations/eQTLCatalogue/v0.1/Homo_sapiens.GRCh38.96.version_1/*.gff3'\
--tx_fasta /gpfs/hpc/home/a72094/annotations/eQTLCatalogue/v0.1/gencode.v30.transcripts.fa