nextflow run meripseqpipe
-profile docker
--genome GRCh37
--single_end 1
--readPaths 'SRP012098/SRR*/*fastq'
--designfile 'metadata/meripmanifest.txt'
--comparefile 'metadata/comparefile.txt'
--aligners star
--peakCalling_mode independence
--peakMerged_mode rank
--expression_analysis_mode DESeq2
--methylation_analysis_mode QNB
--fasta refs/GRCh37.p13.genome.fa
--gtf refs/gencode.v19.annotation.gtf
--max_cpus 4
--max_memory '19GB'
--reads 'SRP012098/SRR*/*fastq' \