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docker.config
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docker.config
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params {
/*
User setting options (mandatory)
*/
// input file and genome reference()
fastq_ext = '*_{1,2}.fq.gz'
fasta_ref = '/data/database/hg38/genome.fa'
design = 'design.file' // or null
hisat2_index = '/data/database/hg38/hisatIndex/grch38_snp_tran/genome_snp_tran'
cpatpath='/opt/CPAT-1.2.3'
//human gtf only
gencode_annotation_gtf = "/data/database/hg38/Annotation/gencode.v24.annotation.gtf"
lncipedia_gtf = "/data/database/hg38/Annotation/lncipedia_4_0_hg38.gtf" // set "null" if you are going to perform analysis on other species
/*
User setting options (optional)
*/
// tools setting
hisat_strand = 'RF'
star_index = ''//set if star used
bowtie2_index = ''//set if tophat used
aligner = "hisat" // or "star","tophat"
sam_processor="sambamba"//or "samtools(deprecated)"
qctools ="fastp" // or "afterqc","fastp","fastqc","none" to skip qc step
detools = "edger"//or "deseq2"
quant = "kallisto"// or 'htseq'
//other setting
singleEnd = false
unstrand = false
skip_combine = false
lncRep_Output = 'reporter.html'
lncRep_theme = 'npg'
lncRep_cdf_percent = 10
lncRep_max_lnc_len = 10000
lncRep_min_expressed_sample = 50
mem=60
cpu=30
/*
for non-human setting
*/
species="human"// mouse , zebrafish, fly
known_coding_gtf=""
known_lncRNA_gtf=""
/*
Don't modify
*/
cpatpath ='/opt/CPAT-1.2.3'
}
/*
Don't modify either
*/
// Docker options
docker.runOptions = '-u $(id -u):$(id -g)'
docker.enabled = true
process.container = 'bioinformatist/lncpipe:latest'
// individual process setting
process.cache = 'deep'
process {
withLabel: para {
maxForks = 6
}
withLabel: 'qc' {
maxForks = 6
}
}
manifest {
homePage = 'https//github.com/likelet/LncPipe'
description = 'LncPipe:a Nextflow-based Long non-coding RNA analysis PIPELINE'
mainScript = 'LncRNAanalysisPipe.nf'
}