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nextflow.config
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nextflow.config
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params {
cpus = 16
mapping_memory = '50GB'
index_cpus = cpus
mapping_cpus = cpus
counting_cpus = cpus
gtf_URL="ftp://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens/Homo_sapiens.GRCh38.101.chr.gtf.gz"
genome_URL="ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome"
samples = ['SRR628582','SRR628583','SRR628584','SRR628585','SRR628586','SRR628587','SRR628588','SRR628589']
chr = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16' , '17', '18', '19', '20', '21', '22', 'MT', 'X', 'Y']
}
process {
withName:fastqDump {
container = "./containers/sratoolkit/sra.sif"
}
withName:index {
container = "./containers/star/star.sif"
}
withName:mapping {
cpus = 14
container = "./containers/star/star.sif"
}
withName:samtoolsIndex {
container = "./containers/samtools/samtools.sif"
}
withName:countingReads {
container = "./containers/featurecounts/featcount.sif"
}
withName:DESeq{
container = "docker://evolbioinfo/deseq2:v1.28.1"
}
}
singularity.enabled = true