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 thefasterq
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']
- default=
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
- default
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
- default
sjdbOverhang
(a STAR-specific parameter.default=99
)- For further information about this parameter, see this tutorial, or the STAR manual.