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nerdstrike/annotated_function_central.json

Last active April 23, 2021 11:02
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Resource specifications in npg_seq_pipeline graph
Raw
annotated_function_central.json
{
"graph" : {
"label" : "NPG sequence pipeline job dependency graph",
"metadata": { "description": "Perhaps we could put pipeline defaults here?" },
"edges" : [...],
"nodes" : [
{
"id" : "pipeline_start",
"label" : "pipeline_start",
"metadata": {
"description": "Beginning of pipeline. JSON does not allow comments",
"resources": {}
}
},
{
"id" : "create_summary_link_analysis",
"label" : "create_summary_link_analysis",
"metadata": {
"description": "stuff",
"resources": {
"default": {
"queue": "small"
}
}
}
},
{
"id" : "run_analysis_in_progress",
"label" : "run_analysis_in_progress",
"metadata": {
"description": "Mark pipeline state as in progress",
"resources" : {}
}
},
{
"id" : "lane_analysis_in_progress",
"label" : "lane_analysis_in_progress",
...
},
{
"id" : "qc_interop",
"label" : "qc_interop",
"metadata": {
"description": "AutoQC interop",
"resources": {
"defaults": {
"minimum_cpu": 8,
"memory": 2
}
}
}
},
{
"id" : "p4_stage1_analysis",
"label" : "p4_stage1_analysis",
"metadata": {
"description": "Create CRAM files including initial phiX alignment, spatial filtering and deplexing of pools where appropriate.",
"resources": {
"default": {
"minimum_cpu": 8,
"maximum_cpu": 16,
"memory": 12,
"fs_slots_num": 4,
"queue": "p4stage1"
}
}
}
},
{
"id" : "stage2pp",
"label" : "stage2pp",
"metadata": {
"description": "Create portable pipeline scaffold and definitions",
"resources": {}
}
},
{
"id" : "stage2App",
"label" : "stage2App",
"metadata": {
"description": "Create Amplicon scaffold and definitions",
"resources": {}
}
},
{
"id" : "update_ml_warehouse_1",
"label" : "update_ml_warehouse",
"metadata": {
"description": "Something something warehouse",
"resources": {
"default": {
"db": ["mlwh"]
}
}
}
},
{
"id" : "update_ml_warehouse_2",
"label" : "update_ml_warehouse",
...
},
{
"id" : "update_ml_warehouse_3",
"label" : "update_ml_warehouse",
...
},
{
"id" : "run_secondary_analysis_in_progress",
"label" : "run_secondary_analysis_in_progress"
},
{
"id" : "qc_generic_artic",
"label" : "qc_generic_artic",
"metadata": {
"description": "Run ncov2019 artic NextFlow pipeline",
"resources": {
"default": {
"minimum_cpu": 4,
"memory": 5
}
}
}
},
{
"id" : "qc_generic_ampliconstats",
"label" : "qc_generic_ampliconstats",
"metadata": {
"description": "Create ampliconstats via artic NextFlow pipeline",
"resources": {
"default": {
"minimum_cpu": 2,
"memory": 1
}
}
}
},
{
"id" : "qc_qX_yield",
"label" : "qc_qX_yield"
},
{
"id" : "qc_adapter",
"label" : "qc_adapter",
"metadata": {
"description": "Check for adapter contamination",
"resources": {
"default": {
"memory": 1.5,
"minimum_cpu": 3
}
}
}
},
{
"id" : "qc_insert_size",
"label" : "qc_insert_size",
"metadata": {
"description": "Perform a paired-end alignment to find insert size",
"resources": {
"default": {
"memory": 8
}
}
}
},
{
"id" : "qc_sequence_error",
"label" : "qc_sequence_error"
},
{
"id" : "qc_gc_fraction",
"label" : "qc_gc_fraction"
},
{
"id" : "qc_ref_match",
"label" : "qc_ref_match",
"metadata": {
"description": "Determine which species a sample may come from, based on alignment",
"resources": {
"default": {
"memory": 6,
"maximum_cpu": 8,
"array_cpu_limit": 8
}
}
}
},
{
"id" : "seq_alignment",
"label" : "seq_alignment",
"metadata": {
"description": "Align against a reference",
"resources": {
"default": {
"minimum_cpu": 12,
"maximum_cpu": 16,
"memory": 32,
"fs_slots_num": 4
},
"star": {
"memory": 38
}
}
}
},
{
"id" : "bam_cluster_counter_check",
"label" : "bam_cluster_counter_check"
},
{
"id" : "seqchksum_comparator",
"label" : "seqchksum_comparator"
},
{
"id" : "qc_bcfstats",
"label" : "qc_bcfstats"
},
{
"id" : "qc_pulldown_metrics",
"label" : "qc_pulldown_metrics"
},
{
"id" : "qc_genotype",
"label" : "qc_genotype"
},
{
"id" : "qc_spatial_filter",
"label" : "qc_spatial_filter"
},
{
"id" : "qc_verify_bam_id",
"label" : "qc_verify_bam_id"
},
{
"id" : "qc_review",
"label" : "qc_review"
},
{
"id" : "run_analysis_complete",
"label" : "run_analysis_complete"
},
{
"id" : "archive_pp_data_to_irods",
"label" : "archive_pp_data_to_irods"
},
{
"id" : "archive_to_irods_samplesheet",
"label" : "archive_to_irods_samplesheet",
"metadata" : {
"description": "Publish data to iRods with samplesheet LIMS driver",
"resources": {
"default": {
"reserve_irods_slots" : 1,
"fs_slots_num": 1,
"queue": "lowload"
}
}
}
},
{
"id" : "bqsr_calc",
"label" : "bqsr_calc"
},
{
"id" : "haplotype_caller",
"label" : "haplotype_caller"
},
{
"id" : "merge_recompress",
"label" : "merge_recompress"
},
{
"id" : "run_qc_review_pending",
"label" : "run_qc_review_pending"
},
{
"id" : "pipeline_end",
"label" : "pipeline_end"
}
]
}
}
Raw
function_list_central.json
{
"graph" : {
"edges" : [...],
"nodes" : [
{
"id" : "pipeline_start",
"label" : "pipeline_start"
},
{
"id" : "create_summary_link_analysis",
"label" : "create_summary_link_analysis"
},
{
"id" : "run_analysis_in_progress",
"label" : "run_analysis_in_progress"
},
{
"id" : "lane_analysis_in_progress",
"label" : "lane_analysis_in_progress"
},
{
"id" : "qc_interop",
"label" : "qc_interop"
},
{
"id" : "p4_stage1_analysis",
"label" : "p4_stage1_analysis"
},
{
"id" : "stage2pp",
"label" : "stage2pp"
},
{
"id" : "stage2App",
"label" : "stage2App"
},
{
"id" : "update_ml_warehouse_1",
"label" : "update_ml_warehouse"
},
{
"id" : "update_ml_warehouse_2",
"label" : "update_ml_warehouse"
},
{
"id" : "update_ml_warehouse_3",
"label" : "update_ml_warehouse"
},
{
"id" : "run_secondary_analysis_in_progress",
"label" : "run_secondary_analysis_in_progress"
},
{
"id" : "qc_generic_artic",
"label" : "qc_generic_artic"
},
{
"id" : "qc_generic_ampliconstats",
"label" : "qc_generic_ampliconstats"
},
{
"id" : "qc_qX_yield",
"label" : "qc_qX_yield"
},
{
"id" : "qc_adapter",
"label" : "qc_adapter"
},
{
"id" : "qc_insert_size",
"label" : "qc_insert_size"
},
{
"id" : "qc_sequence_error",
"label" : "qc_sequence_error"
},
{
"id" : "qc_gc_fraction",
"label" : "qc_gc_fraction"
},
{
"id" : "qc_ref_match",
"label" : "qc_ref_match"
},
{
"id" : "seq_alignment",
"label" : "seq_alignment"
},
{
"id" : "bam_cluster_counter_check",
"label" : "bam_cluster_counter_check"
},
{
"id" : "seqchksum_comparator",
"label" : "seqchksum_comparator"
},
{
"id" : "qc_bcfstats",
"label" : "qc_bcfstats"
},
{
"id" : "qc_pulldown_metrics",
"label" : "qc_pulldown_metrics"
},
{
"id" : "qc_genotype",
"label" : "qc_genotype"
},
{
"id" : "qc_spatial_filter",
"label" : "qc_spatial_filter"
},
{
"id" : "qc_verify_bam_id",
"label" : "qc_verify_bam_id"
},
{
"id" : "qc_review",
"label" : "qc_review"
},
{
"id" : "run_analysis_complete",
"label" : "run_analysis_complete"
},
{
"id" : "archive_pp_data_to_irods",
"label" : "archive_pp_data_to_irods"
},
{
"id" : "archive_to_irods_samplesheet",
"label" : "archive_to_irods_samplesheet"
},
{
"id" : "bqsr_calc",
"label" : "bqsr_calc"
},
{
"id" : "haplotype_caller",
"label" : "haplotype_caller"
},
{
"id" : "merge_recompress",
"label" : "merge_recompress"
},
{
"id" : "run_qc_review_pending",
"label" : "run_qc_review_pending"
},
{
"id" : "pipeline_end",
"label" : "pipeline_end"
}
]
}
}
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