SOFT : NextflowWorkflows
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Site du soft: https://nf-co.re/
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LICENSE:
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MIT
See software documentation for more informations.


Location: /usr/local/bioinfo/src/NextflowWorkflows
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Load binaries and environment:
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-> 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:
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/usr/local/bioinfo/src/NextflowWorkflows/example_on_cluster


Quick start:
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-> 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:
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See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.