Merge pull request #203 from SpatialHackathon/wip_wf_optargs

change access so snakemake can proceed
SpatialHackathon · Feb 14, 2024 · 6b296b0 · 6b296b0
2 parents 45fc8f1 + 65d0ea0
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diff --git a/method/BANKSY/banksy.yml b/method/BANKSY/banksy.yml
diff --git a/method/BANKSY/banksy_env.sh b/method/BANKSY/banksy_env.sh
diff --git a/method/BANKSY/banksy_optargs.json b/method/BANKSY/banksy_optargs.json
diff --git a/method/BayesSpace/BayesSpace.yml b/method/BayesSpace/BayesSpace.yml
diff --git a/method/BayesSpace/BayesSpace_optargs.json b/method/BayesSpace/BayesSpace_optargs.json
diff --git a/method/DRSC/DRSC.yml b/method/DRSC/DRSC.yml
diff --git a/method/DRSC/DRSC_optargs.json b/method/DRSC/DRSC_optargs.json
diff --git a/method/DRSC/drsc_env.sh b/method/DRSC/drsc_env.sh
diff --git a/method/DeepST/DeepST.yml b/method/DeepST/DeepST.yml
diff --git a/method/DeepST/DeepST_optargs.json b/method/DeepST/DeepST_optargs.json
diff --git a/method/GraphST/GraphST.yml b/method/GraphST/GraphST.yml
diff --git a/method/GraphST/GraphST_optargs.json b/method/GraphST/GraphST_optargs.json
diff --git a/method/GraphST/method_GraphST.py b/method/GraphST/method_GraphST.py
diff --git a/method/SC.MEB/SC.MEB.yml b/method/SC.MEB/SC.MEB.yml
diff --git a/method/SC.MEB/SC.MEB_optargs.json b/method/SC.MEB/SC.MEB_optargs.json
diff --git a/method/SC.MEB/scmeb_env.sh b/method/SC.MEB/scmeb_env.sh
diff --git a/method/SCAN-IT/config.json b/method/SCAN-IT/config.json
diff --git a/method/SCAN-IT/method_scanit.py b/method/SCAN-IT/method_scanit.py
diff --git a/method/SCAN-IT/scanit.yml b/method/SCAN-IT/scanit.yml
diff --git a/method/SCAN-IT/scanit_optargs.json b/method/SCAN-IT/scanit_optargs.json
diff --git a/method/SEDR/SEDR.yml b/method/SEDR/SEDR.yml
diff --git a/method/SEDR/SEDR_optargs.json b/method/SEDR/SEDR_optargs.json
diff --git a/method/SOTIP/method_sotip.py b/method/SOTIP/method_sotip.py
diff --git a/method/SOTIP/sotip.yml b/method/SOTIP/sotip.yml
diff --git a/method/SOTIP/sotip_optargs.json b/method/SOTIP/sotip_optargs.json
diff --git a/method/STAGATE/STAGATE.yml b/method/STAGATE/STAGATE.yml
diff --git a/method/STAGATE/STAGATE_optargs.json b/method/STAGATE/STAGATE_optargs.json
diff --git a/method/STAGATE/method_STAGATE.py b/method/STAGATE/method_STAGATE.py
diff --git a/method/SpaceFlow/method_spaceflow.py b/method/SpaceFlow/method_spaceflow.py
diff --git a/method/SpaceFlow/spaceflow.yml b/method/SpaceFlow/spaceflow.yml
diff --git a/method/SpaceFlow/spaceflow_optargs.json b/method/SpaceFlow/spaceflow_optargs.json
diff --git a/method/SpiceMix/README.md b/method/SpiceMix/README.md
diff --git a/method/SpiceMix/SpiceMix.py b/method/SpiceMix/SpiceMix.py
diff --git a/method/SpiceMix/SpiceMix.yml b/method/SpiceMix/SpiceMix.yml
diff --git a/method/SpiceMix/SpiceMix_optargs.json b/method/SpiceMix/SpiceMix_optargs.json
diff --git a/method/bass/bass.yml b/method/bass/bass.yml
diff --git a/method/bass/bass_env.sh b/method/bass/bass_env.sh
diff --git a/method/bass/bass_optargs.json b/method/bass/bass_optargs.json
diff --git a/method/maple/maple.yml b/method/maple/maple.yml
diff --git a/method/maple/maple_env.sh b/method/maple/maple_env.sh
diff --git a/method/maple/maple_optargs.json b/method/maple/maple_optargs.json
diff --git a/method/meringue/meringue.yml b/method/meringue/meringue.yml
diff --git a/method/meringue/meringue_env.sh b/method/meringue/meringue_env.sh
diff --git a/method/meringue/meringue_optargs.json b/method/meringue/meringue_optargs.json
diff --git a/method/precast/precast.yml b/method/precast/precast.yml
diff --git a/method/precast/precast_env.sh b/method/precast/precast_env.sh
diff --git a/method/precast/precast_optargs.json b/method/precast/precast_optargs.json
diff --git a/method/scanpy/method_scanpy.py b/method/scanpy/method_scanpy.py
diff --git a/method/scanpy/scanpy_env.yaml b/method/scanpy/scanpy_env.yaml
diff --git a/method/scanpy/scanpy_optargs.json b/method/scanpy/scanpy_optargs.json
diff --git a/method/seurat/seurat.yml b/method/seurat/seurat.yml
diff --git a/method/seurat/seurat_optargs.json b/method/seurat/seurat_optargs.json
diff --git a/method/spaGCN/spaGCN.yml b/method/spaGCN/spaGCN.yml
diff --git a/method/spaGCN/spaGCN_optargs.json b/method/spaGCN/spaGCN_optargs.json
diff --git a/method/stardust/stardust.yml b/method/stardust/stardust.yml
diff --git a/method/stardust/stardust_env.sh b/method/stardust/stardust_env.sh
diff --git a/method/stardust/stardust_optargs.json b/method/stardust/stardust_optargs.json
diff --git a/metric/ARI/ARI.yml b/metric/ARI/ARI.yml
diff --git a/metric/ARI/ARI_optargs.json b/metric/ARI/ARI_optargs.json
diff --git a/metric/CHAOS/CHAOS.r b/metric/CHAOS/CHAOS.r
diff --git a/metric/CHAOS/CHAOS.yml b/metric/CHAOS/CHAOS.yml
diff --git a/metric/CHAOS/CHAOS_optargs.json b/metric/CHAOS/CHAOS_optargs.json
diff --git a/metric/Calinski-Harabasz/Calinski-Harabasz.py b/metric/Calinski-Harabasz/Calinski-Harabasz.py
diff --git a/metric/Calinski-Harabasz/Calinski-Harabasz.yml b/metric/Calinski-Harabasz/Calinski-Harabasz.yml
diff --git a/metric/Calinski-Harabasz/Calinski-Harabasz_optargs.json b/metric/Calinski-Harabasz/Calinski-Harabasz_optargs.json
diff --git a/metric/Completeness/Completeness.py b/metric/Completeness/Completeness.py
diff --git a/metric/Completeness/Completeness.yml b/metric/Completeness/Completeness.yml
diff --git a/metric/Completeness/Completeness_optargs.json b/metric/Completeness/Completeness_optargs.json
diff --git a/metric/Davies-Bouldin/Davies-Bouldin.py b/metric/Davies-Bouldin/Davies-Bouldin.py
diff --git a/metric/Davies-Bouldin/Davies-Bouldin.yml b/metric/Davies-Bouldin/Davies-Bouldin.yml
diff --git a/metric/Davies-Bouldin/Davies-Bouldin_optargs.json b/metric/Davies-Bouldin/Davies-Bouldin_optargs.json
diff --git a/metric/Entropy/Entropy.py b/metric/Entropy/Entropy.py
diff --git a/metric/Entropy/Entropy.yml b/metric/Entropy/Entropy.yml
diff --git a/metric/Entropy/Entropy_optargs.json b/metric/Entropy/Entropy_optargs.json
diff --git a/metric/FMI/FMI.py b/metric/FMI/FMI.py
diff --git a/metric/FMI/FMI.yml b/metric/FMI/FMI.yml
diff --git a/metric/FMI/FMI_optargs.json b/metric/FMI/FMI_optargs.json
diff --git a/metric/Homogeneity/Homogeneity.py b/metric/Homogeneity/Homogeneity.py
diff --git a/metric/Homogeneity/Homogeneity.yml b/metric/Homogeneity/Homogeneity.yml
diff --git a/metric/Homogeneity/Homogeneity_optargs.json b/metric/Homogeneity/Homogeneity_optargs.json
diff --git a/metric/LISI/LISI.r b/metric/LISI/LISI.r
diff --git a/metric/LISI/LISI.yml b/metric/LISI/LISI.yml
diff --git a/metric/LISI/LISI_optargs.json b/metric/LISI/LISI_optargs.json
diff --git a/metric/MCC/MCC.py b/metric/MCC/MCC.py
diff --git a/metric/MCC/MCC.yaml b/metric/MCC/MCC.yaml
diff --git a/metric/MCC/MCC_optargs.json b/metric/MCC/MCC_optargs.json
diff --git a/metric/NMI/NMI.yml b/metric/NMI/NMI.yml
diff --git a/metric/NMI/NMI_optargs.json b/metric/NMI/NMI_optargs.json
diff --git a/metric/PAS/PAS.r b/metric/PAS/PAS.r
diff --git a/metric/PAS/PAS.yml b/metric/PAS/PAS.yml
diff --git a/metric/PAS/PAS_optargs.json b/metric/PAS/PAS_optargs.json
diff --git a/metric/V_measure/V_measure.yml b/metric/V_measure/V_measure.yml
diff --git a/metric/V_measure/V_measure_optargs.json b/metric/V_measure/V_measure_optargs.json
diff --git a/metric/cluster-specific-silhouette/cluster-specific-silhouette.yml b/metric/cluster-specific-silhouette/cluster-specific-silhouette.yml
diff --git a/metric/cluster-specific-silhouette/cluster-specific-silhouette_optargs.json b/metric/cluster-specific-silhouette/cluster-specific-silhouette_optargs.json
diff --git a/metric/domain-specific-f1/domain-specific-f1.yml b/metric/domain-specific-f1/domain-specific-f1.yml
diff --git a/metric/domain-specific-f1/domain-specific-f1_optargs.json b/metric/domain-specific-f1/domain-specific-f1_optargs.json
diff --git a/metric/jaccard/jaccard.py b/metric/jaccard/jaccard.py
diff --git a/metric/jaccard/jaccard.yaml b/metric/jaccard/jaccard.yaml
diff --git a/metric/jaccard/jaccard_optargs.json b/metric/jaccard/jaccard_optargs.json