mobile_elements/nextflow.config at main · Timniem/mobile_elements · GitHub

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env {
  TMPDIR = "\${TMPDIR:-\${NXF_TEMP:-\$(mktemp -d)}}"
  APPTAINER_DISABLE_CACHE = "True"

  CMD_SCRAMBLE = "apptainer exec ${projectDir}/containers/scramble.sif"
  CMD_MELT = "apptainer exec ${projectDir}/containers/melt.sif"

}

process {
    executor = "slurm"
    errorStrategy = 'ignore'
    containerOptions = "--bind ${projectDir}"
}

params {
    // genomebuild: hg19 or hg38 (default)
    genomeBuild="hg38"
    reference_genome = "/groups/umcg-gdio/tmp02/umcg-tniemeijer/resources/reference/GRCh38_full_analysis_set_plus_decoy_hla.fa"
    samplesheet = "/groups/umcg-gdio/tmp02/umcg-tniemeijer/resources/sampletables/test_melt_hg38.tsv"
    output = "/groups/umcg-gdio/tmp02/umcg-tniemeijer/melt_scramble/output/test_hg38"

    scramble {
      cluster_analysis_folder = "${projectDir}/resources/scramble/scramble/cluster_analysis"
      cluster_analysis_bin = "${params.scramble.cluster_analysis_folder}/bin"
      scramble_script = "${params.scramble.cluster_analysis_bin}/SCRAMble.R"
      mei_ref = "${cluster_analysis_folder}/resources/MEI_consensus_seqs.fa"
    }
    melt {
      melt_jar = "${projectDir}/resources/melt/MELTv2.2.2/MELT.jar"
      genes_bed_hg19 = "${projectDir}/resources/melt/MELTv2.2.2/add_bed_files/1KGP_Hg19/hg19.genes.bed"
      genes_bed_hg38 = "${projectDir}/resources/melt/MELTv2.2.2/add_bed_files/Hg38/Hg38.genes.bed"
      transposon_file_list_hg19 = "${projectDir}/resources/melt/hg19_transposon_file_list.txt"
      transposon_file_list_hg38 = "${projectDir}/resources/melt/hg38_transposon_file_list.txt"
    }

}

workDir="${params.output}/work"