cluster.eichler.json

{
    "__default__": {
        "params": "-l mfree=1G -l h_rt=00:30:00"
    },
    "prepare_tuple_count_table_for_reference": {"params": "-l mfree=8G -l h_rt=00:30:00"},
    "prepare_suffix_array_for_reference": {"params": "-l mfree=40G -l h_rt=08:00:00"},
    "index_reference": {"params": "-l mfree=16G -l h_rt=08:00:00"},
    "plot_alignment_summaries": {"params": "-l mfree=8G -l h_rt=00:15:00"},
    "align_batch": {"params": "-l h_rt=48:00:00 -l disk_free=10G -l mfree=8.25G -pe serial 8 -N align_batch"},
    "annotate_coverage_for_candidates": {"params": "-l mfree=10G -l h_rt=01:00:00"},
    "identify_gaps_in_reference_assembly": {"params": "-l h_rt=04:00:00 -l mfree=2G"},
    "collect_hardstops": {"params": "-l mfree=4G -l h_rt=01:00:00"},
    "find_hardstops_in_aligned_reads": {"params": "-l mfree=4G -l h_rt=04:00:00"},
    "annotate_coverage_of_merged_gap_support": {"params": "-l mfree=5G -l h_rt=01:00:00"},
    "find_gaps_in_aligned_reads": {"params": "-l mfree=6G -l disk_free=1G -l h_rt=04:00:00"},
    "merge_coverage_per_batch": {"params": "-l mfree=1G -l h_rt=08:00:00"},
    "calculate_coverage_per_batch": {"params": "-l mfree=4G -l h_rt=04:00:00"},
    "assemble_region": {"params": "-l mfree=12G -pe serial 1 -l disk_free=10G -l h_rt=01:00:00"},
    "collect_assembly_alignments": {"params": "-l mfree=30G -l disk_free=10G -l h_rt=01:00:00"},
    "find_inversions": {"params": "-pe serial 8 -l mfree=2G -l h_rt=03:00:00"},
    "tile_contigs_from_alignments": {"params": "-l h_rt=01:00:00"},
    "find_calls_by_gaps_in_alignments": {"params": "-l h_rt=02:00:00"},
    "identify_calls_by_type": {"params": "-l h_rt=02:00:00 -l mfree=8G"},
    "repeatmask_sv_fasta": {"params": "-l h_rt=06:00:00 -pe serial 8 -l mfree=5G"},
    "trf_mask_sv_fasta": {"params": "-l h_rt=01:00:00 -l mfree=2G"},
    "find_indel_gaps_in_alignments": {"params": "-l h_rt=02:00:00"},
    "filter_indel_gaps_by_tiling_path": {"params": "-l mfree=4G -l h_rt=00:30:00"},
    "calculate_coverage_from_assembled_contigs": {"params": "-l mfree=12G -l h_rt=01:00:00"},
    "annotate_coverage_of_assembled_contigs_for_indels": {"params": "-l h_rt=01:00:00"},
    "annotate_coverage_of_pacbio_reads_for_indels": {"params": "-l h_rt=01:00:00"},
    "find_snvs_alignments": {"params": "-l h_rt=02:00:00"},
    "map_sv_sequences_to_bam_reference": {"params": "-l h_rt=02:00:00 -l mfree=33G -R y"},
    "find_positions_of_sv_sequences_in_bam_reference": {"params": "-l h_rt=01:00:00"},
    "merge_reference_and_local_assemblies": {"params": "-l h_rt=01:00:00"},
    "bwa_index_combined_reference": {"params": "-l mfree=10G -l h_rt=06:00:00"},
    "map_sample_reads": {"params": "-l mfree=4G -pe serial 12 -l disk_free=17G -l h_rt=24:00:00 -R y -l ssd=FALSE"},
    "calculate_depth_across_PacBio_SVs": {"params": "-l h_rt=06:00:00 -l mfree=4G"},
    "genotype_across_all_samples": {"params": "-l h_rt=00:30:00 -l mfree=2G"},
    "convert_genotypes_to_vcf": {"params": "-l h_rt=00:30:00 -l mfree=4G"}
}