RiboKastIndex/config.yaml at main · Transipedia/RiboKastIndex · GitHub

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# -----------------------------------------------------------------
#                      RiboKastIndex Configuration
# -----------------------------------------------------------------
project_name: "RiboKastIndex"

# -----------------------------------------------------------------
#                      Path Settings
# -----------------------------------------------------------------
paths:
  # Root directory of the project (write it once)
  local_path: "/store/EQUIPES/SSFA/MEMBERS/safa.maddouri/RiboKastIndex_test/"

  # Everything below is relative to local_path
  RibokastIndex_tools: "tools/"
  results_path: "RESULTS/"
  stats_path: "stats/"
  logs_path: "logs/"
  snakemake_log_path: ".snakemake/log/"
  fastq_path: "fastq/"
  conda_env: "RiboKastIndex.yaml"

# -----------------------------------------------------------------
#                      Reference Files
# -----------------------------------------------------------------
fasta: "human.fa"
gff: "human.gff3"
fasta_outRNA: "rRNA.fasta"

# -----------------------------------------------------------------
#                      Adapter Trimming Settings
# -----------------------------------------------------------------
already_trimmed: "no"
adapt_sequence: ""

# -----------------------------------------------------------------
#                      Length Selection for Profiling
# -----------------------------------------------------------------
readsLength_min: "25"
readsLength_max: "35"

# -----------------------------------------------------------------
#                      GFF File Settings
# -----------------------------------------------------------------
gff_cds_feature: "CDS"
gff_mRNA_feature: "mRNA"
gff_5UTR_feature: "five_prime_UTR"
gff_parent_attribut: "Parent"
gff_name_attribut: "Name"

# -----------------------------------------------------------------
#                      riboWaltz Analysis Settings
# -----------------------------------------------------------------
kmercount_pct_threshold: "60"

# -----------------------------------------------------------------
#                      K-mer Index Construction Settings
# -----------------------------------------------------------------
pathJoinCounts: "$PATH:/data/work/I2BC/safa.maddouri/tools/dekupl-joinCounts"

kmerSize: "25"
mode: "phase"          # normal | phase

forced_phase: 12
# forced_phase: null

kamrat_normalize: true
kamrat_nfbase: 1000000

kamratImg: "/store/EQUIPES/SSFA/MEMBERS/safa.maddouri/KaMRaT.sif"