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schema: '2.0'
stages:
inspect_tools@utilities:
cmd:
- mkdir -p results/tooling
- singularity run --app manifest toolbox/bin/utilities.sif >results/tooling/utilities.manifest
- singularity run --app specification toolbox/bin/utilities.sif 9ec8df2a1ad7633ed0893527ca1c8c4f56426ab868a0adccea366a9fbf799898
>results/tooling/utilities.specification
deps:
- path: toolbox/bin/utilities.sif
md5: bcc60b742c50c9b3c7ac466d653e2487
size: 26841088
outs:
- path: results/tooling/utilities.manifest
md5: ea94e4e836054dbf5b074d8fcc5c3fcc
size: 691751
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
acquire_data:
cmd:
- mkdir -p results
- singularity exec toolbox/bin/utilities.sif wget -O results/raw-inputs.zip https://ndownloader.figshare.com/files/26052149
deps:
- path: https://ndownloader.figshare.com/files/26052149
checksum: '"9ec0859fba86ca208118b92ebea977b2"'
size: 51926003
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
outs:
- path: results/raw-inputs.zip
md5: 9ec0859fba86ca208118b92ebea977b2
size: 51926003
extract_Yang_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/extract_data.sh results/raw-inputs.zip
"noise_GRN_share/bulk_Yang/*" results/raw/Yang
deps:
- path: results/raw-inputs.zip
md5: 9ec0859fba86ca208118b92ebea977b2
size: 51926003
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
outs:
- path: results/raw/Yang
md5: 717f50b83204bd005e95a81af740ab8d.dir
size: 21588641
nfiles: 11
clean_Yang_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/clean_Yang.sh results/raw/Yang
results/clean/Yang
deps:
- path: results/raw/Yang
md5: 717f50b83204bd005e95a81af740ab8d.dir
size: 21588641
nfiles: 11
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
- path: src/clean_Yang.sh
md5: 03335834f78bcbf998a1a58261e50b61
size: 485
outs:
- path: results/clean/Yang
md5: 612f9167ca9ae3826517602309691430.dir
size: 3572827
nfiles: 7
inspect_tools@Rmultitool:
cmd:
- mkdir -p results/tooling
- singularity run --app manifest toolbox/bin/R-multitool.sif >results/tooling/R-multitool.manifest
- singularity run --app specification toolbox/bin/R-multitool.sif adc703754189748fa75be2a4ec9f317f39409cfaf08eee163d7f8f59c6b511d1
>results/tooling/R-multitool.specification
deps:
- path: toolbox/bin/R-multitool.sif
md5: bc82f33c01b13bf11ad1c71f8698e701
size: 770953216
outs:
- path: results/tooling/R-multitool.manifest
md5: dc3df55d91790360a46e4788b246cf8a
size: 31350
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
denoise_Yang_data:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/denoise.sh results/clean/Yang
counts_raw.csv results/denoised/Yang logs/denoised/Yang
deps:
- path: results/clean/Yang
md5: 612f9167ca9ae3826517602309691430.dir
size: 3572827
nfiles: 7
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/denoise.R
md5: e225c6bb7e080f691f20fed4f7000711
size: 899
- path: src/denoise.sh
md5: 2943d4aba67e432331a1c1c6925ac630
size: 313
outs:
- path: results/denoised/Yang
md5: 460fc635e0bc67e7f8e7a8868847ffd6.dir
size: 13851757
nfiles: 9
slice_Yang_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh results/denoised/Yang
results/sliced/Yang
deps:
- path: results/denoised/Yang
md5: 460fc635e0bc67e7f8e7a8868847ffd6.dir
size: 13851757
nfiles: 9
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
- path: src/slice.sh
md5: b8c2aebb69164ab9c85b755ae42ba22e
size: 409
outs:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
inspect_tools@NetworkInferenceJl:
cmd:
- mkdir -p results/tooling
- singularity run --app manifest toolbox/bin/NetworkInference.jl.sif >results/tooling/NetworkInference.jl.manifest
- singularity run --app specification toolbox/bin/NetworkInference.jl.sif 3e491ce8057710cc2f0cf020b178f6315889e1b19357716b5f0da301475f9098
>results/tooling/NetworkInference.jl.specification
deps:
- path: toolbox/bin/NetworkInference.jl.sif
md5: ae0aa7af639b3170a4fec7a3299a3e67
size: 376860672
outs:
- path: results/tooling/NetworkInference.jl.manifest
md5: 52899d0750870deebbdd60a3397e5e7d
size: 11932
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
infer@Yang/NetworkInference.jl/PIDC:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Yang results/networks/Yang/NetworkInference.jl/PIDC logs/networks/Yang/NetworkInference.jl/PIDC
julia src/inference/NetworkInference.jl/infer_network.jl PIDC
deps:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Yang/NetworkInference.jl/PIDC
md5: d44ebf3bd6def39939c1c30e42fb92b7.dir
size: 236779444
nfiles: 20
infer@Yang/NetworkInference.jl/CLR:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Yang results/networks/Yang/NetworkInference.jl/CLR logs/networks/Yang/NetworkInference.jl/CLR
julia src/inference/NetworkInference.jl/infer_network.jl CLR
deps:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Yang/NetworkInference.jl/CLR
md5: 430510c3e62be2d361b5e4f2d88827f2.dir
size: 227389786
nfiles: 20
extract_Cuomo_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/extract_data.sh results/raw-inputs.zip
"noise_GRN_share/SC_Cuomo/*" results/raw/Cuomo
deps:
- path: results/raw-inputs.zip
md5: 9ec0859fba86ca208118b92ebea977b2
size: 51926003
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
outs:
- path: results/raw/Cuomo
md5: f0143ff3cb97ab3c5c3b9530b3ea3931.dir
size: 446579167
nfiles: 11
clean_Cuomo_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/clean_Cuomo.sh results/raw/Cuomo
results/clean/Cuomo
deps:
- path: results/raw/Cuomo
md5: f0143ff3cb97ab3c5c3b9530b3ea3931.dir
size: 446579167
nfiles: 11
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
- path: src/clean_Cuomo.sh
md5: 5c6a3271d13cc48289d294ca64c35323
size: 407
outs:
- path: results/clean/Cuomo
md5: 0c27f5ad071ac55d3ea29f4e41ee33a4.dir
size: 32982591
nfiles: 4
denoise_Cuomo_data:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/denoise.sh results/clean/Cuomo
counts_raw_day2.csv results/denoised/Cuomo logs/denoised/Cuomo
deps:
- path: results/clean/Cuomo
md5: 0c27f5ad071ac55d3ea29f4e41ee33a4.dir
size: 32982591
nfiles: 4
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/denoise.R
md5: e225c6bb7e080f691f20fed4f7000711
size: 899
- path: src/denoise.sh
md5: 2943d4aba67e432331a1c1c6925ac630
size: 313
outs:
- path: results/denoised/Cuomo
md5: df4978ec76edf2021462ac9c2f0b9b33.dir
size: 191741510
nfiles: 7
slice_Cuomo_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh results/denoised/Cuomo
results/sliced/Cuomo
deps:
- path: results/denoised/Cuomo
md5: df4978ec76edf2021462ac9c2f0b9b33.dir
size: 191741510
nfiles: 7
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
- path: src/slice.sh
md5: b8c2aebb69164ab9c85b755ae42ba22e
size: 409
outs:
- path: results/sliced/Cuomo
md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
size: 7478152
nfiles: 12
infer@Cuomo/NetworkInference.jl/PUC:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Cuomo results/networks/Cuomo/NetworkInference.jl/PUC logs/networks/Cuomo/NetworkInference.jl/PUC
julia src/inference/NetworkInference.jl/infer_network.jl PUC
deps:
- path: results/sliced/Cuomo
md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
size: 7478152
nfiles: 12
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Cuomo/NetworkInference.jl/PUC
md5: 383f7ee94db0b759d14a182e70358dbd.dir
size: 16345552
nfiles: 12
fuse_Yang_data:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/fuse_samples_foreach.sh
results/denoised/Yang results/clean/Yang/samples.csv results/fused/Yang
deps:
- path: results/clean/Yang
md5: 612f9167ca9ae3826517602309691430.dir
size: 3572827
nfiles: 7
- path: results/denoised/Yang
md5: 460fc635e0bc67e7f8e7a8868847ffd6.dir
size: 13851757
nfiles: 9
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/fuse_samples.R
md5: 3351b6a733b256c9d0463044aef0f8a9
size: 819
- path: src/fuse_samples_foreach.sh
md5: 5aee33d8918c59b2f746bc1c7723e0e8
size: 305
outs:
- path: results/fused/Yang
md5: 899074e95c3cc77759b8a19775890e4f.dir
size: 9326957
nfiles: 9
infer@Cuomo/NetworkInference.jl/PIDC:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Cuomo results/networks/Cuomo/NetworkInference.jl/PIDC logs/networks/Cuomo/NetworkInference.jl/PIDC
julia src/inference/NetworkInference.jl/infer_network.jl PIDC
deps:
- path: results/sliced/Cuomo
md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
size: 7478152
nfiles: 12
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Cuomo/NetworkInference.jl/PIDC
md5: a4a4c79e0f10665a2dc2012d70bfabb2.dir
size: 16525252
nfiles: 12
infer@Cuomo/NetworkInference.jl/MI:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Cuomo results/networks/Cuomo/NetworkInference.jl/MI logs/networks/Cuomo/NetworkInference.jl/MI
julia src/inference/NetworkInference.jl/infer_network.jl MI
deps:
- path: results/sliced/Cuomo
md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
size: 7478152
nfiles: 12
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Cuomo/NetworkInference.jl/MI
md5: 9052973b1c536239944542b1412b5598.dir
size: 16852278
nfiles: 12
analyze@Cuomo/NetworkInference.jl/MI:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Cuomo/NetworkInference.jl/MI results/analysis/Cuomo/NetworkInference.jl/MI
logs/analysis/Cuomo/NetworkInference.jl/MI Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Cuomo/NetworkInference.jl/MI
md5: 9052973b1c536239944542b1412b5598.dir
size: 16852278
nfiles: 12
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Cuomo/NetworkInference.jl/MI
md5: 40f4d9ef2a77d8e871d4fed614ac226c.dir
size: 82831001
nfiles: 54
infer@Yang/NetworkInference.jl/MI:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Yang results/networks/Yang/NetworkInference.jl/MI logs/networks/Yang/NetworkInference.jl/MI
julia src/inference/NetworkInference.jl/infer_network.jl MI
deps:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Yang/NetworkInference.jl/MI
md5: 9697f8ebb89d825e0c3210f98d648fc2.dir
size: 244914282
nfiles: 20
infer@Cuomo/GENIE3-R:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Cuomo results/networks/Cuomo/GENIE3-R logs/networks/Cuomo/GENIE3-R
Rscript src/inference/GENIE3-R/infer_network.R
deps:
- path: results/sliced/Cuomo
md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
size: 7478152
nfiles: 12
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/inference/GENIE3-R
md5: a5df150e6e7d5e031ba6de4be3c27d86.dir
size: 238
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Cuomo/GENIE3-R
md5: fac15bf7c2889c4a7b559bd57cffeac7.dir
size: 6477552
nfiles: 12
analyze@Cuomo/GENIE3-R:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Cuomo/GENIE3-R results/analysis/Cuomo/GENIE3-R logs/analysis/Cuomo/GENIE3-R
Rscript src/analysis/analyze_for_network_variants.R src/analysis/data_variants.csv
src/analysis/load_genie3r_network.function.R png
deps:
- path: results/networks/Cuomo/GENIE3-R
md5: fac15bf7c2889c4a7b559bd57cffeac7.dir
size: 6477552
nfiles: 12
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_genie3r_network.function.R
md5: 12202df92a0152f558c694b549de95f2
size: 277
outs:
- path: results/analysis/Cuomo/GENIE3-R
md5: b6a83af6ac6fc5df0d8e6f09b53738ee.dir
size: 71745391
nfiles: 54
inspect_tools@arboreto:
cmd:
- mkdir -p results/tooling
- singularity run --app manifest toolbox/bin/arboreto.sif >results/tooling/arboreto.manifest
- singularity run --app specification toolbox/bin/arboreto.sif 540b9a053e4d862bfab972735d1d62af04485c186cf5735e98748ef5b5f8b27f
>results/tooling/arboreto.specification
deps:
- path: toolbox/bin/arboreto.sif
md5: b694f240a16512ff448830734d7d8267
size: 1122693120
outs:
- path: results/tooling/arboreto.manifest
md5: 4ebe1904f00a80abe10c5bd09f509d79
size: 12757
- path: results/tooling/arboreto.specification
md5: 793af50d330ba258602678040a1f76c9
size: 239
analyze@Yang/NetworkInference.jl/CLR:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Yang/NetworkInference.jl/CLR results/analysis/Yang/NetworkInference.jl/CLR
logs/analysis/Yang/NetworkInference.jl/CLR Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Yang/NetworkInference.jl/CLR
md5: 430510c3e62be2d361b5e4f2d88827f2.dir
size: 227389786
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Yang/NetworkInference.jl/CLR
md5: 2eeaf1c368a78db981e7365c29ae463d.dir
size: 209575109
nfiles: 90
infer@Yang/LEAP:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Yang results/networks/Yang/LEAP logs/networks/Yang/LEAP Rscript
src/inference/LEAP/infer_network.R
deps:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/inference/LEAP
md5: 708b4f57275adfbe4a1202fcf7d76dec.dir
size: 658
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Yang/LEAP
md5: a75ba4ee43804ba0e3cf61ba4ccc2f79.dir
size: 292310714
nfiles: 20
analyze@Yang/LEAP:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Yang/LEAP results/analysis/Yang/LEAP logs/analysis/Yang/LEAP
Rscript src/analysis/analyze_for_network_variants.R src/analysis/data_variants.csv
src/analysis/load_leap_network.function.R png
deps:
- path: results/networks/Yang/LEAP
md5: a75ba4ee43804ba0e3cf61ba4ccc2f79.dir
size: 292310714
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_leap_network.function.R
md5: 3a4deadcf36f7b44c533a641bf06d38c
size: 410
outs:
- path: results/analysis/Yang/LEAP
md5: f7ed3231c129c2327e78c6a89b8e1109.dir
size: 436003759
nfiles: 90
analyze@Yang/NetworkInference.jl/MI:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Yang/NetworkInference.jl/MI results/analysis/Yang/NetworkInference.jl/MI
logs/analysis/Yang/NetworkInference.jl/MI Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Yang/NetworkInference.jl/MI
md5: 9697f8ebb89d825e0c3210f98d648fc2.dir
size: 244914282
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Yang/NetworkInference.jl/MI
md5: 84060e96a436e59775525d8f074f4067.dir
size: 186851937
nfiles: 90
infer@Cuomo/GRNBoost2:
cmd: singularity exec toolbox/bin/arboreto.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Cuomo results/networks/Cuomo/GRNBoost2 logs/networks/Cuomo/GRNBoost2
python src/inference/GRNBoost2/infer_network.py
deps:
- path: results/sliced/Cuomo
md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
size: 7478152
nfiles: 12
- path: results/tooling/arboreto.specification
md5: 793af50d330ba258602678040a1f76c9
size: 239
- path: src/inference/GRNBoost2
md5: e8d853b083d8ce1a7a98c1184e3859ef.dir
size: 299
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Cuomo/GRNBoost2
md5: 8542dd75b9d0f1cd66bd468e28eb2228.dir
size: 15548499
nfiles: 12
analyze@Cuomo/GRNBoost2:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Cuomo/GRNBoost2 results/analysis/Cuomo/GRNBoost2 logs/analysis/Cuomo/GRNBoost2
Rscript src/analysis/analyze_for_network_variants.R src/analysis/data_variants.csv
src/analysis/load_grnboost2_network.function.R png
deps:
- path: results/networks/Cuomo/GRNBoost2
md5: 8542dd75b9d0f1cd66bd468e28eb2228.dir
size: 15548499
nfiles: 12
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_grnboost2_network.function.R
md5: 74f8b4b818ad944073f6f7af210b5e7a
size: 404
outs:
- path: results/analysis/Cuomo/GRNBoost2
md5: 55288e1727c51f56cad49a357f4d8c60.dir
size: 66951939
nfiles: 54
analyze@Cuomo/NetworkInference.jl/PIDC:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Cuomo/NetworkInference.jl/PIDC results/analysis/Cuomo/NetworkInference.jl/PIDC
logs/analysis/Cuomo/NetworkInference.jl/PIDC Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Cuomo/NetworkInference.jl/PIDC
md5: a4a4c79e0f10665a2dc2012d70bfabb2.dir
size: 16525252
nfiles: 12
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Cuomo/NetworkInference.jl/PIDC
md5: 36e389b0488a0610a8d81720b3e8cfff.dir
size: 88009320
nfiles: 54
analyze@Yang/NetworkInference.jl/PIDC:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Yang/NetworkInference.jl/PIDC results/analysis/Yang/NetworkInference.jl/PIDC
logs/analysis/Yang/NetworkInference.jl/PIDC Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Yang/NetworkInference.jl/PIDC
md5: d44ebf3bd6def39939c1c30e42fb92b7.dir
size: 236779444
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Yang/NetworkInference.jl/PIDC
md5: 7cc5ead449c985f040023727dbb8c062.dir
size: 251442515
nfiles: 90
infer@Yang/GRNBoost2:
cmd: singularity exec toolbox/bin/arboreto.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Yang results/networks/Yang/GRNBoost2 logs/networks/Yang/GRNBoost2
python src/inference/GRNBoost2/infer_network.py
deps:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
- path: results/tooling/arboreto.specification
md5: 793af50d330ba258602678040a1f76c9
size: 239
- path: src/inference/GRNBoost2
md5: e8d853b083d8ce1a7a98c1184e3859ef.dir
size: 299
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Yang/GRNBoost2
md5: 1cb1305dc237aab8e4477c5220a946ce.dir
size: 247741328
nfiles: 20
analyze@Yang/GRNBoost2:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Yang/GRNBoost2 results/analysis/Yang/GRNBoost2 logs/analysis/Yang/GRNBoost2
Rscript src/analysis/analyze_for_network_variants.R src/analysis/data_variants.csv
src/analysis/load_grnboost2_network.function.R png
deps:
- path: results/networks/Yang/GRNBoost2
md5: 1cb1305dc237aab8e4477c5220a946ce.dir
size: 247741328
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_grnboost2_network.function.R
md5: 74f8b4b818ad944073f6f7af210b5e7a
size: 404
outs:
- path: results/analysis/Yang/GRNBoost2
md5: b9ed4922bf4fae444490b0559e19df86.dir
size: 228326345
nfiles: 90
analyze@Cuomo/NetworkInference.jl/PUC:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Cuomo/NetworkInference.jl/PUC results/analysis/Cuomo/NetworkInference.jl/PUC
logs/analysis/Cuomo/NetworkInference.jl/PUC Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Cuomo/NetworkInference.jl/PUC
md5: 383f7ee94db0b759d14a182e70358dbd.dir
size: 16345552
nfiles: 12
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Cuomo/NetworkInference.jl/PUC
md5: 75e097f5ec0c01368456af38bda23e3f.dir
size: 89193170
nfiles: 54
infer@Cuomo/NetworkInference.jl/CLR:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Cuomo results/networks/Cuomo/NetworkInference.jl/CLR logs/networks/Cuomo/NetworkInference.jl/CLR
julia src/inference/NetworkInference.jl/infer_network.jl CLR
deps:
- path: results/sliced/Cuomo
md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
size: 7478152
nfiles: 12
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Cuomo/NetworkInference.jl/CLR
md5: a3faa73487e276436e69da841aa24fe7.dir
size: 14570496
nfiles: 12
analyze@Cuomo/NetworkInference.jl/CLR:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Cuomo/NetworkInference.jl/CLR results/analysis/Cuomo/NetworkInference.jl/CLR
logs/analysis/Cuomo/NetworkInference.jl/CLR Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Cuomo/NetworkInference.jl/CLR
md5: a3faa73487e276436e69da841aa24fe7.dir
size: 14570496
nfiles: 12
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Cuomo/NetworkInference.jl/CLR
md5: 977bac4853791bbfb56a2a4547d8e509.dir
size: 75057238
nfiles: 54
infer@Yang/GENIE3-R:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Yang results/networks/Yang/GENIE3-R logs/networks/Yang/GENIE3-R
Rscript src/inference/GENIE3-R/infer_network.R
deps:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/inference/GENIE3-R
md5: a5df150e6e7d5e031ba6de4be3c27d86.dir
size: 238
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Yang/GENIE3-R
md5: 7962864c2a3baa9b6fa69600764036c2.dir
size: 99903969
nfiles: 20
analyze@Yang/GENIE3-R:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Yang/GENIE3-R results/analysis/Yang/GENIE3-R logs/analysis/Yang/GENIE3-R
Rscript src/analysis/analyze_for_network_variants.R src/analysis/data_variants.csv
src/analysis/load_genie3r_network.function.R png
deps:
- path: results/networks/Yang/GENIE3-R
md5: 7962864c2a3baa9b6fa69600764036c2.dir
size: 99903969
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_genie3r_network.function.R
md5: 12202df92a0152f558c694b549de95f2
size: 277
outs:
- path: results/analysis/Yang/GENIE3-R
md5: 090c28fcc894c3684f1e3336c1c571c6.dir
size: 334283403
nfiles: 90
slice_Yang_fused_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh results/fused/Yang
results/sliced_fused/Yang
deps:
- path: results/fused/Yang
md5: 899074e95c3cc77759b8a19775890e4f.dir
size: 9326957
nfiles: 9
- path: results/tooling/utilities.specification
md5: b478b6629042ca3693e49bf237d67f5d
size: 82
- path: src/slice.sh
md5: b8c2aebb69164ab9c85b755ae42ba22e
size: 409
outs:
- path: results/sliced_fused/Yang
md5: 33cc1a9c9fc24b31d9a0b6c5b13999ce.dir
size: 562860
nfiles: 20
infer@Yang/NetworkInference.jl/PUC:
cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
results/sliced/Yang results/networks/Yang/NetworkInference.jl/PUC logs/networks/Yang/NetworkInference.jl/PUC
julia src/inference/NetworkInference.jl/infer_network.jl PUC
deps:
- path: results/sliced/Yang
md5: 064657575d70e478626ee2dec21d62f0.dir
size: 864057
nfiles: 20
- path: results/tooling/NetworkInference.jl.specification
md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
size: 373
- path: src/inference/NetworkInference.jl
md5: c238c0ef87689cb377e3ced160111648.dir
size: 371
nfiles: 1
- path: src/inference/infer_foreach_slice.sh
md5: 417599e24e01a117745f41d89c23ef8f
size: 1176
outs:
- path: results/networks/Yang/NetworkInference.jl/PUC
md5: 1fddd3b6db11d786f62a876a8feabed3.dir
size: 240811142
nfiles: 20
analyze@Yang/NetworkInference.jl/PUC:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/Yang/NetworkInference.jl/PUC results/analysis/Yang/NetworkInference.jl/PUC
logs/analysis/Yang/NetworkInference.jl/PUC Rscript src/analysis/analyze_for_network_variants.R
src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
png
deps:
- path: results/networks/Yang/NetworkInference.jl/PUC
md5: 1fddd3b6db11d786f62a876a8feabed3.dir
size: 240811142
nfiles: 20
- path: results/tooling/R-multitool.specification
md5: bc675df8f8747327eb77a58fb0301770
size: 503
- path: src/analysis/analyze_for_network_variants.R
md5: 51d10c7d0647b5a5eb857187b935ec07
size: 6960
- path: src/analysis/analyze_foreach_slice.sh
md5: 2b1512007db296a19161a7d3663bf3b6
size: 1334
- path: src/analysis/data_variants.csv
md5: 006662e316eb55017e1deb28132e1b6f
size: 243
- path: src/analysis/load_network_inference_jl_network.function.R
md5: 680649f2a2d86d406e0e96713e296e98
size: 492
outs:
- path: results/analysis/Yang/NetworkInference.jl/PUC
md5: 17ce1b667a9feea864752325e21318f1.dir
size: 267090538
nfiles: 90