Chapter 5 Parameters

  • index_cpus (number of cpus reserved for the genome indexation process. default=14)
  • mapping_cpus (idem. for the mapping process, used to create BAM files. default=14)
  • counting_cpus (idem. for the counting process. default=7)
  • mapping_memory (RAM reserved for mapping. default=50GB)

If you already possess some of the files needed to execute the pipeline, you can specify them as follows:

  • reads (path pointing to a directory containing the fasterq files)
  • genome (path pointing to a directory containing the genome FASTA file)
  • index (Répertoire contenant les fichiers d’index)
  • mapping (Répertoire contenant les fichiers BAM)
  • counting (Chemin d’accès entier au fichier de comptage – comprend le fichier lui-même)
  • metadata (Chemin d’accès entier au fichier de métadonnées – comprend le fichier lui-même)

If unspecified, the pipeline will be executed using default values from the config file : nextflow.config. These too, can be tweaked and overriden:

  • ids List of SRR accession number to fetch paired-end fastq files.
    • default=['SRR628582', 'SRR628583', 'SRR628584', 'SRR628585', 'SRR628586', 'SRR628587', 'SRR628588', 'SRR628589']
  • genome_url URL to download the reference genome.
    • default ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
  • annotation_url URL to donwload the reference genome’s annotation.
    • default ftp://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens/Homo_sapiens.GRCh38.101.chr.gtf.gz
  • sjdbOverhang (a STAR-specific parameter. default=99)