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cluster.eichler.json
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{
"__default__": {
"mem": "1G",
"cpu": "1",
"rt": "00:30:00",
"params": ""
},
"ref_make_fai": {
"mem": "4G",
"rt": "01:00:00"
},
"ref_make_sa": {
"mem": "40G",
"rt": "08:00:00"
},
"ref_make_ctab": {
"mem": "8G",
"rt": "00:30:00"
},
"aln_align_batch": {
"mem": "8.25G",
"rt": "5:00:00:00",
"cpu": "8",
"params": "-l disk_free=10G"
},
"detect_get_regions": {
"mem": "10G",
"rt": "01:00:00"
},
"detect_stops_ref_gaps": {
"mem": "2G",
"rt": "04:00:00"
},
"detect_stops_merge_batches": {
"mem": "4G",
"rt": "01:00:00"
},
"detect_stops_find_hardstops": {
"mem": "4G",
"rt": "04:00:00"
},
"detect_gaps_annotate_coverage": {
"mem": "24G",
"rt": "04:00:00"
},
"detect_gaps_search": {
"mem": "8G",
"rt": "08:00:00",
"params": "-l disk_free=2G"
},
"detect_merge_coverage": {
"mem": "4G",
"rt": "10:00:00"
},
"detect_coverage_per_batch": {
"mem": "4G",
"rt": "04:00:00"
},
"asm_assemble_group": {
"mem": "{params.mem}",
"cpu": "{params.threads}",
"rt": "{params.rt}",
"params": "-l disk_free=2G"
},
"asm_merge_groups": {
"mem": "2.5G",
"rt": "4:00:00"
},
"call_find_inversions": {
"mem": "4G",
"cpu": "8",
"rt": "05:00:00"
},
"call_tile_contigs_from_alignments": {
"rt": "01:00:00"
},
"call_find_calls_by_gaps_in_alignments": {
"rt": "02:00:00"
},
"call_identify_calls_by_type": {
"mem": "8G",
"rt": "02:00:00"
},
"call_repeatmask_sv_fasta": {
"mem": "5G",
"cpu": "8",
"rt": "06:00:00"
},
"call_trf_mask_sv_fasta": {
"mem": "2G",
"rt": "01:00:00"
},
"call_find_indel_gaps_in_alignments": {
"rt": "02:00:00"
},
"call_filter_indel_gaps_by_tiling_path": {
"mem": "4G"
},
"call_calculate_coverage_from_assembled_contigs": {
"mem": "12G",
"rt": "01:00:00"
},
"call_annotate_coverage_of_assembled_contigs_for_indels": {
"rt": "01:00:00"
},
"call_annotate_coverage_of_pacbio_reads_for_indels": {
"rt": "01:00:00"
},
"call_find_snvs_alignments": {
"rt": "02:00:00"
},
"gt_vcf_fixup": {
"mem": "1G",
"rt": "8:00:00"
},
"gt_vcf_merge": {
"mem": "12G",
"rt": "48:00:00"
},
"gt_vcf_get_sample_column": {
"mem": "2G",
"rt": "8:00:00"
},
"gt_call_sample_breakpoint_depth": {
"mem": "4G",
"rt": "48:00:00"
},
"gt_call_sample_insert_delta": {
"mem": "4G",
"rt": "08:00:00"
},
"gt_call_sample_read_depth": {
"mem": "4G",
"rt": "48:00:00"
},
"gt_contig_bam_to_fasta": {
"mem": "24G",
"rt": "02:00:00"
},
"gt_altref_index": {
"mem": "16G",
"rt": "02:00:00:00",
"params": "-R y -l ssd=TRUE"
},
"gt_map_sample_reads": {
"mem": "{params.mem}",
"cpu": "{params.threads}",
"rt": "{params.rt}",
"params": "-l disk_free={params.disk_free} -R y"
},
"gt_altref_alt_info_bed": {
"mem": "8G",
"rt": "02:00:00"
},
"gt_learn_cv_run": {
"mem": "2G",
"cpu": "4",
"rt": "01:00:00:00"
},
"gt_learn_model_train": {
"mem": "2G",
"cpu": "4",
"rt": "01:00:00:00"
}
}