Commits · 79c92609556dbb48581e02981f428a7092e31408 · omnibenchmark / omni_batch / mnn_omni_batch

24 Jan, 2022 35 commits

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=inverse --set d-10=20 --set · 79c92609

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_20_none_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_20_none_20_inverse_corrected_counts.mtx.gz
csf_patient

renku-transaction: edd1cbf3d0534820bb2f85579c5ed0bf

79c92609

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=inverse --set d-10=20 --set · 05bff60e

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_20_sig_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_20_sig_20_inverse_corrected_counts.mtx.gz
csf_patient

renku-transaction: a4f8c9ba71b946a59e4f5d41a3548651

05bff60e

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=inverse --set d-10=10 --set · 101c4736

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_10_none_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_10_none_20_inverse_corrected_counts.mtx.gz
csf_patient

renku-transaction: 25e339a19ce84cb7b3c37199e47d9b3a

101c4736

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=inverse --set d-10=10 --set · 21d6f12a

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_10_sig_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_10_sig_20_inverse_corrected_counts.mtx.gz
csf_patient

renku-transaction: 91c1e65059394168a8014fa64baacfa8

21d6f12a

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=size --set d-10=20 --set · 223cf184

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_20_none_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_20_none_20_size_corrected_counts.mtx.gz
csf_patient

renku-transaction: 96213eb9cdde463c9f35b8cc26ab21e9

223cf184

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=size --set d-10=20 --set · ecc6f7e9

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_20_sig_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_20_sig_20_size_corrected_counts.mtx.gz csf_patient

renku-transaction: 25cf8e8f51e544caadd323c0458db082

ecc6f7e9

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=size --set d-10=10 --set · b7926fb8

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_10_none_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_10_none_20_size_corrected_counts.mtx.gz
csf_patient

renku-transaction: 406961f7ca4e4ff0b8adffcc3f1fd11d

b7926fb8

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=size --set d-10=10 --set · 7e46817d

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/csf_patient_10_sig_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/csf_patient_10_sig_20_size_corrected_counts.mtx.gz csf_patient

renku-transaction: ae565f86d4954b4d9a8309530b5e7ad1

7e46817d

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=auto --set d-10=20 --set · 40504108

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_20_none_20_auto_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_20_none_20_auto_corrected_counts.mtx.gz cellbench

renku-transaction: aac6a252eda743779fe6f790b634441c

40504108

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=auto --set d-10=20 --set · 30c60b38

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_20_sig_20_auto_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_20_sig_20_auto_corrected_counts.mtx.gz cellbench

renku-transaction: c58f146fa90a4c64a4611b879ae8a91c

30c60b38

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=auto --set d-10=10 --set · 51cb3fc4

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_10_none_20_auto_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_10_none_20_auto_corrected_counts.mtx.gz cellbench

renku-transaction: 4def7bd09a2a441b975937ffbe5f592d

51cb3fc4

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=auto --set d-10=10 --set · d7b5c544

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_10_sig_20_auto_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_10_sig_20_auto_corrected_counts.mtx.gz cellbench

renku-transaction: b4c7765a44c24c349a128c0972519371

d7b5c544

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=inverse --set d-10=20 --set · b3ac3951

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_20_none_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_20_none_20_inverse_corrected_counts.mtx.gz cellbench

renku-transaction: 3de1960027924d39aafa86596bff2852

b3ac3951

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=inverse --set d-10=20 --set · 650c7097

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_20_sig_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_20_sig_20_inverse_corrected_counts.mtx.gz cellbench

renku-transaction: 456593c65b0648e7890bbdebbcf3cb6d

650c7097

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=inverse --set d-10=10 --set · 4ee6c7a5

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_10_none_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_10_none_20_inverse_corrected_counts.mtx.gz cellbench

renku-transaction: 44b02f38d3924bf991e706eb9cd67d53

4ee6c7a5

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=inverse --set d-10=10 --set · 2149478e

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_10_sig_20_inverse_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_10_sig_20_inverse_corrected_counts.mtx.gz cellbench

renku-transaction: 70afe0481b4c4c9e968cb964c5cf4a9b

2149478e

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=size --set d-10=20 --set · 51446546

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_20_none_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_20_none_20_size_corrected_counts.mtx.gz cellbench

renku-transaction: 21393e9c78c84e3da0b937c886186d44

51446546

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=size --set d-10=20 --set · 0fde0751

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_20_sig_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_20_sig_20_size_corrected_counts.mtx.gz cellbench

renku-transaction: 518312fe9c634de4b8ded5c8796b2a5d

0fde0751

renku workflow execute --set k-8=20 --set hvg-11=none --set order-5=size --set d-10=10 --set · 2dd06ec5

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_10_none_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_10_none_20_size_corrected_counts.mtx.gz cellbench

renku-transaction: 7bbacbafcb034f169540e012f2e9f0e1

2dd06ec5

renku workflow execute --set k-8=20 --set hvg-11=sig --set order-5=size --set d-10=10 --set · c7d8d108

Almut Luetge authored Jan 24, 2022

corrected_dim_file-2=data/omni_batch_mnn/cellbench_10_sig_20_size_red_dim.mtx.gz --set
corrected_counts-3=data/omni_batch_mnn/cellbench_10_sig_20_size_corrected_counts.mtx.gz cellbench

renku-transaction: a359f23bb5d44c43b7b41cf5f5c1e63c

c7d8d108

Saved changes to: src/workflow/param_files/mnn_wflow_params.json · 4bdd15dd
Almut Luetge authored Jan 24, 2022

4bdd15dd

renku run --name csf_patient --input src/mnn.R --input · 18d55697

Almut Luetge authored Jan 24, 2022

	data/omni_batch_processed/norm_counts_csf_patient.mtx.gz --input
	data/omni_batch_processed/hvg_csf_patient.json --input
	data/omni_batch_processed/meta_csf_patient.json -- Rscript --vanilla src/mnn.R
	--corrected_dim_file=data/omni_batch_mnn/csf_patient_20_sig_10_auto_red_dim.mtx.gz
	--corrected_counts=data/omni_batch_mnn/csf_patient_20_sig_10_auto_corrected_counts.mtx.gz
	--dataset_name=csf_patient --order=auto --hvg_file=data/omni_batch_processed/hvg_csf_patient.json
	--meta_file=data/omni_batch_processed/meta_csf_patient.json --k=10
	--count_file=data/omni_batch_processed/norm_counts_csf_patient.mtx.gz --d=20 --hvg=sig

renku-transaction: 4f682a24835542d28eaf9621c1c2ae93

18d55697

renku run --name cellbench --input src/mnn.R --input · 45d9a99d

Almut Luetge authored Jan 24, 2022

	data/omni_batch_processed/norm_counts_cellbench.mtx.gz --input
	data/omni_batch_processed/hvg_cellbench.json --input data/omni_batch_processed/meta_cellbench.json --
	Rscript --vanilla src/mnn.R
	--corrected_dim_file=data/omni_batch_mnn/cellbench_20_sig_10_auto_red_dim.mtx.gz
	--corrected_counts=data/omni_batch_mnn/cellbench_20_sig_10_auto_corrected_counts.mtx.gz
	--dataset_name=cellbench --order=auto --hvg_file=data/omni_batch_processed/hvg_cellbench.json
	--meta_file=data/omni_batch_processed/meta_cellbench.json --k=10
	--count_file=data/omni_batch_processed/norm_counts_cellbench.mtx.gz --d=20 --hvg=sig

renku-transaction: 0674986445994da098e0cf83fc4f2a54

45d9a99d

Saved changes to: src/mnn.R · 639a85c0
Almut Luetge authored Jan 24, 2022

639a85c0
Saved changes to: src/mnn.R src/workflow/define_workflow.sh · 32285c7b
Almut Luetge authored Jan 24, 2022

32285c7b
Saved changes to: install.R src/mnn.R · 45e16c25
Almut Luetge authored Jan 24, 2022

45e16c25
Saved changes to: src/mnn.R · c3326f69
Almut Luetge authored Jan 24, 2022

c3326f69
Saved changes to: src/workflow/param_files/mnn_params.json · e7ea1168
Almut Luetge authored Jan 24, 2022
```
	src/workflow/param_files/mnn_params_filtered.json
	src/workflow/param_files/mnn_params_thresholds.json
```
e7ea1168
Saved changes to: src/config.sh · 2d0dbea0
Almut Luetge authored Jan 24, 2022

2d0dbea0
Saved changes to: src/workflow/param_files/mnn_params.json · d404b48d
Almut Luetge authored Jan 24, 2022
```
	src/workflow/param_files/mnn_params_filtered.json
	src/workflow/param_files/mnn_params_thresholds.json
```
d404b48d
Saved changes to: src/config.sh · 914f3953
Almut Luetge authored Jan 24, 2022

914f3953

Saved changes to: src/workflow/param_files/mnn_excl_params.json · c247c5eb

Almut Luetge authored Jan 24, 2022

	src/workflow/param_files/mnn_params.json
	src/workflow/param_files/mnn_params_filtered.json
	src/workflow/param_files/mnn_params_thresholds.json

c247c5eb

renku dataset update omni_batch_params · 29c8c2d2
Almut Luetge authored Jan 24, 2022
```
renku-transaction: 240cff7566724ce1a9d724c874e88f6b
```
29c8c2d2
renku dataset update omni_batch_processed · 39103e00
Almut Luetge authored Jan 24, 2022
```
renku-transaction: 3c69e355a85f484db7bcbbcf7f3dacdb
```
39103e00
Saved changes to: src/config.sh src/mnn.R src/run_mnn.sh src/workflow/define_workflow.sh · 79812408
Almut Luetge authored Jan 24, 2022

79812408

23 Jan, 2022 1 commit
- Update utils. · ac73bf0b
  Almut Luetge authored Jan 23, 2022
  
  ac73bf0b
20 Jan, 2022 4 commits
- Saved changes to: data/omni_batch_mnn/cellbench_auto_NULL_20_30_reconstruct.mtx.gz · de482a21
  Almut Luetge authored Jan 20, 2022
```
	data/omni_batch_mnn/cellbench_auto_NULL_20_30_red_dim.mtx.gz
	data/omni_batch_mnn/csf_patient_auto_NULL_20_30_reconstruct.mtx.gz
	data/omni_batch_mnn/csf_patient_auto_NULL_20_30_red_dim.mtx.gz
```
  de482a21
- renku workflow remove csf_patient · f271ecd8
  Almut Luetge authored Jan 20, 2022
```
renku-transaction: 913796cc3ee34488bd3731ef12131894
```
  f271ecd8
- renku workflow remove cellbench · 0ead3182
  Almut Luetge authored Jan 20, 2022
```
renku-transaction: 282849f2f363471bbd8acd54a3055c3d
```
  0ead3182
- renku dataset unlink -I data/omni_batch_mnn/* omni_batch_mnn · dcef5053
  Almut Luetge authored Jan 20, 2022
```
renku-transaction: ba6785cf0c544211b7be9d233cccc3e7
```
  dcef5053