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janursajanursa
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grn evaluation was addded pathway args
1 parent 021cd8a commit 336175e

4 files changed

Lines changed: 62 additions & 31 deletions

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‎scripts/run_all.sh‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
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set -e
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datasets=( 'replogle' 'op' 'nakatake' 'adamson' 'norman' 'xaira_HEK293T' 'xaira_HCT116' 'parsebioscience' 'ibd_uc' 'ibd_cd' '300BCG' ) #'replogle' 'op' 'nakatake' 'adamson' 'norman' 'xaira_HEK293T' 'xaira_HCT116' 'parsebioscience' 'ibd_uc' 'ibd_cd' '300BCG') #
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# datasets=( 'ibd_uc' 'ibd_cd' ) #'replogle' 'op' 'nakatake' 'adamson' 'norman' 'xaira_HEK293T' 'xaira_HCT116' 'parsebioscience' 'ibd_uc' 'ibd_cd' '300BCG') #
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datasets=( 'replogle' 'op' ) #'replogle' 'op' 'nakatake' 'adamson' 'norman' 'xaira_HEK293T' 'xaira_HCT116' 'parsebioscience' 'ibd_uc' 'ibd_cd' '300BCG') #
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run_local=false # set to true to run locally, false to run on AWS
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run_grn_inference=false
@@ -56,7 +56,7 @@ for dataset in "${datasets[@]}"; do
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fi
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echo "Running GRN evaluation for dataset: $dataset"
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# bash scripts/run_grn_evaluation.sh --dataset=$dataset --run_local=$run_local --build_images=false
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bash scripts/run_grn_evaluation.sh --dataset=$dataset --run_local=$run_local --build_images=false
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fi
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if [ "$run_download" = true ]; then

‎src/utils/dataset_config.env‎

Lines changed: 13 additions & 11 deletions
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@@ -10,17 +10,19 @@ CELLTYPE_xaira_HCT116="HCT116"
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CELLTYPE_op="PBMC"
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CELLTYPE_parsebioscience="PBMC"
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CELLTYPE_300BCG="PBMC"
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CELLTYPE_ibd="PBMC"
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CELLTYPE_ibd_uc="PBMC"
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CELLTYPE_ibd_cd="PBMC"
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CELLTYPE_nakatake=""
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# Metrics (comma-separated)
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METRICS_replogle="regression,ws_distance,tf_recovery,tf_binding"
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METRICS_adamson="regression,ws_distance,tf_binding"
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METRICS_norman="regression,ws_distance,tf_binding"
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METRICS_nakatake="regression"
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METRICS_op="regression,vc,rc_tf_act,tf_binding"
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METRICS_300BCG="regression,vc,rc_tf_act,tf_binding"
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METRICS_ibd="regression,vc,tf_binding"
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METRICS_parsebioscience="regression,vc,rc_tf_act,tf_binding"
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METRICS_xaira_HEK293T="regression,ws_distance,tf_recovery,tf_binding"
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METRICS_xaira_HCT116="regression,ws_distance,tf_recovery,tf_binding"
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METRICS_replogle="regression,ws_distance,tf_recovery,tf_binding,sem,gs_recovery"
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METRICS_adamson="regression,tf_binding,sem,gs_recovery"
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METRICS_norman="regression,ws_distance,tf_binding,sem,gs_recovery"
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METRICS_nakatake="regression,sem,gs_recovery"
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METRICS_op="regression,vc,rc_tf_act,tf_binding,sem,rc,anchor_regression,gs_recovery"
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METRICS_300BCG="regression,vc,rc_tf_act,tf_binding,sem,rc,anchor_regression,gs_recovery"
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METRICS_ibd_uc="regression,vc,tf_binding,sem,anchor_regression,gs_recovery"
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METRICS_ibd_cd="regression,vc,tf_binding,sem,anchor_regression,gs_recovery"
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METRICS_parsebioscience="regression,vc,rc_tf_act,tf_binding,sem,rc,anchor_regression,gs_recovery"
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METRICS_xaira_HEK293T="regression,ws_distance,tf_recovery,tf_binding,sem,gs_recovery"
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METRICS_xaira_HCT116="regression,ws_distance,tf_recovery,tf_binding,sem,gs_recovery"

src/workflows/run_evaluation/config.vsh.yaml renamed to src/workflows/run_grn_evaluation/config.vsh.yaml

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Original file line numberDiff line numberDiff line change
@@ -71,23 +71,46 @@ argument_groups:
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must_exist: false
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required: false
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example: resources_test/grn_benchmark/prior/ws_distance_background_norman.csv
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# - name: --ground_truth_unibind
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# type: file
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# direction: input
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# must_exist: false
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# required: false
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# - name: --ground_truth_chipatlas
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# type: file
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# direction: input
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# must_exist: false
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# required: false
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# - name: --ground_truth_remap
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# type: file
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# direction: input
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# must_exist: false
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# required: false
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- name: --ground_truth_unibind
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type: file
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direction: input
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must_exist: false
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required: false
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- name: --ground_truth_chipatlas
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type: file
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direction: input
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must_exist: false
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required: false
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- name: --ground_truth_remap
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type: file
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direction: input
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must_exist: false
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required: false
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- name: --geneset_hallmark_2020
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type: file
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required: false
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description: Hallmark 2020 geneset GMT file
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- name: --geneset_kegg_2021
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type: file
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required: false
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description: KEGG 2021 geneset GMT file
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- name: --geneset_reactome_2022
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type: file
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required: false
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description: Reactome 2022 geneset GMT file
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- name: --geneset_go_bp_2023
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type: file
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required: false
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description: GO Biological Process 2023 geneset GMT file
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- name: --geneset_bioplanet_2019
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type: file
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required: false
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description: BioPlanet 2019 geneset GMT file
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- name: --geneset_wikipathways_2019
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type: file
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required: false
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description: WikiPathways 2019 geneset GMT file
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- name: Outputs
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arguments:
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- name: "--scores"

src/workflows/run_evaluation/main.nf renamed to src/workflows/run_grn_evaluation/main.nf

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Original file line numberDiff line numberDiff line change
@@ -62,7 +62,13 @@ workflow run_wf {
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layer: "layer",
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ground_truth_unibind: "ground_truth_unibind",
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ground_truth_chipatlas: "ground_truth_chipatlas",
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ground_truth_remap: "ground_truth_remap"
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ground_truth_remap: "ground_truth_remap",
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geneset_hallmark_2020: "geneset_hallmark_2020",
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geneset_kegg_2021: "geneset_kegg_2021",
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geneset_reactome_2022: "geneset_reactome_2022",
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geneset_go_bp_2023: "geneset_go_bp_2023",
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geneset_bioplanet_2019: "geneset_bioplanet_2019",
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geneset_wikipathways_2019: "geneset_wikipathways_2019"
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],
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// use 'toState' to publish that component's outputs to the overall state
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toState: { id, output, state, comp ->

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