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nextflow.config
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nextflow.config
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docker.enabled = true
params {
// parameters to be passed to scripts
index_cpus = 14
mapping_cpus = 14
counting_cpus = 7
mapping_memory = '50GB'
// optional command-line arguments
reads = null
genome = null
index = null
mapping = null
counting = null
metadata = "SraRunTable.txt"
// default values for automatic (default)
// execution of the pipeline
genome_url = "ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
annotation_url = "ftp://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens/Homo_sapiens.GRCh38.101.chr.gtf.gz"
// genome_url = "http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/Human/GRCh38_Ensembl99_sparseD3_sjdbOverhang99/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
// annotation_url = "http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/Human/GRCh38_Ensembl99_sparseD3_sjdbOverhang99/Homo_sapiens.GRCh38.99.gtf"
// full pipeline execution ids
ids = ['SRR628582', 'SRR628583', 'SRR628584', 'SRR628585', 'SRR628586', 'SRR628587', 'SRR628588', 'SRR628589']
// STAR parameters
sjdbOverhang = 99
}
process {
shell = ['/bin/sh']
executor='local'
withName: Fasterq {
cpus=4
container='staphb/sratoolkit:latest'
echo=false
}
withName: Genome {
cpus=1
echo=false
}
withName: Index {
container='evolbioinfo/star:v2.7.6a'
echo=false
}
withName: Mapping {
echo=false
container='evolbioinfo/star:v2.7.6a'
}
withName: Counting {
echo=false
container='evolbioinfo/subread:v2.0.1'
}
withName: DESeq {
echo=false
container='evolbioinfo/deseq2:v1.28.1'
}
}