SOFT : NextflowWorkflows ------ Site du soft: https://nf-co.re/ ------------- LICENSE: -------- MIT See software documentation for more informations. Location: /usr/local/bioinfo/src/NextflowWorkflows --------- Load binaries and environment: ------------------------------ -> fixer les repertoires a ne faire qu'une fois lors de la premiere utilisation : sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh -> nf-core workflows : module purge module load bioinfo/nfcore-Nextflow-v19.04.0 Example directory for use on cluster: ------------------------------------- /usr/local/bioinfo/src/NextflowWorkflows/example_on_cluster Quick start: ------------ -> nextflow help: nextflow run -h -> rnaseq workflow help: nextflow run nf-core/rnaseq -profile genotoul --help -> rnaseq workflow usage example: nextflow run nf-core/rnaseq -profile genotoul \ --reads '*_{1,2}_Ch6.fastq.gz'\ --fasta mongenome.fasta\ --gtf monannotation.gtf -> methylseq workflow usage example: module load bioinfo/nfcore-Nextflow-v19.04.0 nextflow run nf-core/methylseq -profile genotoul \ --fasta /usr/local/bioinfo/src/NextflowWorkflows/example_on_cluster/data/ITAG2.3_genomic_Ch6.fasta \ --reads '/usr/local/bioinfo/src/NextflowWorkflows/example_on_cluster/data/MT_rep1_{1,2}_Ch6.fastq.gz' -> outputs: Results directories will be create into current directory. To rerun workflow without overwriting allready finished jobs use option -resume -> workflows documentation: See https://github.com/nf-core/ Tested pipeline: ------------ See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.