| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.6a |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.5b (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2b1 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2b |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2a1 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2a |
| rna_starsolo |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| star | 2.7.5b | package |
| samtools | 1.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
soloCBwhitelist: filtered.barcodes.txt input_types|use: repeat refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz solo|params|chemistry: CR3 refGenomeSource|geneSource: history refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf solo|soloStrand: Forward refGenomeSource|sjdbOverhang: 100 solo|soloUMIdedup: 1MM_All refGenomeSource|genomeSAindexNbases: 4 input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz solo|soloFeatures: Gene |
attributes: name attributes: name attributes: name attributes: name attributes: name |
pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf name |
| Test-2 |
soloCBwhitelist: filtered.barcodes.txt input_types|use: repeat solo|params|chemistry: custom refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|geneSource: history refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf solo|soloStrand: Forward solo|params|soloCBlen: 16 refGenomeSource|sjdbOverhang: 100 solo|soloUMIdedup: 1MM_All refGenomeSource|genomeSAindexNbases: 4 solo|params|soloCBstart: 1 input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz solo|params|soloUMIlen: 12 solo|soloFeatures: Gene solo|params|soloUMIstart: 17 |
attributes: name attributes: name attributes: name attributes: name attributes: name |
pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf name |
| Test-3 |
soloCBwhitelist: filtered.barcodes.txt input_types|use: repeat refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz solo|params|chemistry: CR3 refGenomeSource|geneSource: history refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf solo|soloStrand: Forward refGenomeSource|sjdbOverhang: 100 solo|soloUMIdedup: 1MM_All refGenomeSource|genomeSAindexNbases: 4 input_types|input1: ['pbmc_1k_v2_L001.R1.10k.fastq.gz', 'pbmc_1k_v2_L001.R1.10k.fastq.gz', 'pbmc_1k_v2_L001.R1.10k.fastq.gz'] input_types|input2: ['pbmc_1k_v2_L001.R2.10k.fastq.gz', 'pbmc_1k_v2_L001.R2.10k.fastq.gz', 'pbmc_1k_v2_L001.R2.10k.fastq.gz'] solo|soloFeatures: Gene |
attributes: name |
pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf name |
| Test-4 |
soloCBwhitelist: filtered.barcodes.txt input_types|use: list_paired refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz solo|params|chemistry: CR3 refGenomeSource|geneSource: history refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf solo|soloStrand: Forward refGenomeSource|sjdbOverhang: 100 solo|soloUMIdedup: 1MM_All input_types|input_collection: paired collection refGenomeSource|genomeSAindexNbases: 4 solo|soloFeatures: Gene |
attributes: name attributes: name |
pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf name |