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schema: '2.0'
stages:
lyproxify@1:
cmd: "lyscripts data lyproxify -i 2023-clb-multisite/raw.csv -o 2023-clb-multisite/data.csv
-m 2023-clb-multisite/mapping.py -r 0 1 2 --drop-rows 439 --add-index\n"
deps:
- path: 2023-clb-multisite/mapping.py
hash: md5
md5: 3d679466cc60d39b17c3643248ffb85d
size: 28286
- path: 2023-clb-multisite/raw.csv
hash: md5
md5: 07fb62f160142252fe11e1738de6331f
size: 211635
outs:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 2ba19b79a80bf72f444dfe79a5165dc0
size: 113116
description-and-docs@2023-clb-multisite:
cmd: "python scripts/render.py -m 2023-clb-multisite/mapping.py -d 2023-clb-multisite/data.csv
-t 2023-clb-multisite/README.template -o 2023-clb-multisite/README.md\n"
deps:
- path: 2023-clb-multisite/README.template
hash: md5
md5: 4fee1faf0a125c4dc6a9462a6a93fcc4
size: 3295
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 2ba19b79a80bf72f444dfe79a5165dc0
size: 113116
- path: 2023-clb-multisite/mapping.py
hash: md5
md5: 3d679466cc60d39b17c3643248ffb85d
size: 28286
- path: scripts/render.py
hash: md5
md5: f288e59e2380a86708df57be8961d6ed
size: 2004
outs:
- path: 2023-clb-multisite/README.md
hash: md5
md5: f9fb683d2328e2f83ca47d2064790d3b
size: 14600
description-and-docs@2023-isb-multisite:
cmd: "python scripts/render.py -m 2023-isb-multisite/mapping.py -d 2023-isb-multisite/data.csv
-t 2023-isb-multisite/README.template -o 2023-isb-multisite/README.md\n"
deps:
- path: 2023-isb-multisite/README.template
hash: md5
md5: 289ed4bef464a64d84d93126403800a9
size: 3064
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: 2023-isb-multisite/mapping.py
hash: md5
md5: 077ee8c837b587e3fc5b5ee810d0265c
size: 52984
- path: scripts/render.py
hash: md5
md5: f288e59e2380a86708df57be8961d6ed
size: 2004
outs:
- path: 2023-isb-multisite/README.md
hash: md5
md5: 5648913555b260ef67efaca4f9b7f331
size: 19642
lyproxify@0:
cmd: "lyscripts data lyproxify -i 2021-clb-oropharynx/raw.csv -o 2021-clb-oropharynx/data.csv
-m 2021-clb-oropharynx/mapping.py -r 0\n"
deps:
- path: 2021-clb-oropharynx/mapping.py
hash: md5
md5: da65d51377e1204ed366ce28bf9ef944
size: 21401
- path: 2021-clb-oropharynx/raw.csv
hash: md5
md5: ca6413b63f277e4f6bb40b50294b0ff0
size: 96789
outs:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
lyproxify@2:
cmd: "lyscripts data lyproxify -i 2023-isb-multisite/raw.csv -o 2023-isb-multisite/data.csv
-m 2023-isb-multisite/mapping.py -r 0\n"
deps:
- path: 2023-isb-multisite/mapping.py
hash: md5
md5: 077ee8c837b587e3fc5b5ee810d0265c
size: 52984
- path: 2023-isb-multisite/raw.csv
hash: md5
md5: 0546a71875f357e0210425407dedf426
size: 167129
outs:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
description-and-docs@2021-clb-oropharynx:
cmd: "python scripts/render.py -m 2021-clb-oropharynx/mapping.py -d 2021-clb-oropharynx/data.csv
-t 2021-clb-oropharynx/README.template -o 2021-clb-oropharynx/README.md\n"
deps:
- path: 2021-clb-oropharynx/README.template
hash: md5
md5: edf345ea5b29efcee0923cd7fcc43077
size: 16726
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: 2021-clb-oropharynx/mapping.py
hash: md5
md5: da65d51377e1204ed366ce28bf9ef944
size: 21401
- path: scripts/render.py
hash: md5
md5: f288e59e2380a86708df57be8961d6ed
size: 2004
outs:
- path: 2021-clb-oropharynx/README.md
hash: md5
md5: 8dc6c2dfcadc298fb6a6192a211bfc5f
size: 25546
convert-to-docx@2021-clb-oropharynx:
cmd: "pandoc -o ../2021-clb-oropharynx.docx 2021-clb-oropharynx/README.md\n"
deps:
- path: 2021-clb-oropharynx/README.md
md5: f0ec7b542820fc363b43aa635bfe430c
size: 24247
outs:
- path: ../2021-clb-oropharynx.docx
md5: 786537c15c333face3f493a98bfffb03
size: 18743
convert-to-docx@2023-clb-multisite:
cmd: "pandoc -o ../2023-clb-multisite.docx 2023-clb-multisite/README.md\n"
deps:
- path: 2023-clb-multisite/README.md
md5: 49ee462171066d1863ed7801054203d7
size: 13045
outs:
- path: ../2023-clb-multisite.docx
md5: dc1a259586b55abbacb317f04f53dc95
size: 15819
convert-to-docx@2023-isb-multisite:
cmd: "pandoc -o ../2023-isb-multisite.docx 2023-isb-multisite/README.md\n"
deps:
- path: 2023-isb-multisite/README.md
md5: 94299a49ee0cad7483e05ad73a433477
size: 16776
outs:
- path: ../2023-isb-multisite.docx
md5: f7ecf6740c106fcd109e6dfe71ab971d
size: 16747
plot-age-and-sex@2023-clb-multisite:
cmd: "python scripts/age_and_sex.py 2023-clb-multisite/data.csv\n"
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 2ba19b79a80bf72f444dfe79a5165dc0
size: 113116
- path: scripts/age_and_sex.py
hash: md5
md5: e837a45727dd17cb4350ee4c1b1e5676
size: 3212
plot-t-category@2023-clb-multisite:
cmd: "python scripts/t_category.py 2023-clb-multisite/data.csv\n"
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 2ba19b79a80bf72f444dfe79a5165dc0
size: 113116
- path: scripts/t_category.py
hash: md5
md5: 9cd603d2c51bbdb9b9c78f5d6c292914
size: 1647
plot-t-category@2023-isb-multisite:
cmd: "python scripts/t_category.py 2023-isb-multisite/data.csv\n"
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/t_category.py
hash: md5
md5: 9cd603d2c51bbdb9b9c78f5d6c292914
size: 1647
plot-age-and-sex@2021-clb-oropharynx:
cmd: "python scripts/age_and_sex.py 2021-clb-oropharynx/data.csv\n"
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/age_and_sex.py
hash: md5
md5: e837a45727dd17cb4350ee4c1b1e5676
size: 3212
plot-age-and-sex@2023-isb-multisite:
cmd: "python scripts/age_and_sex.py 2023-isb-multisite/data.csv\n"
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/age_and_sex.py
hash: md5
md5: e837a45727dd17cb4350ee4c1b1e5676
size: 3212
plot-t-category@2021-clb-oropharynx:
cmd: "python scripts/t_category.py 2021-clb-oropharynx/data.csv\n"
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/t_category.py
hash: md5
md5: 9cd603d2c51bbdb9b9c78f5d6c292914
size: 1647
plot-t-category@2021-usz-oropharynx:
cmd: "python scripts/t_category.py 2021-usz-oropharynx/data.csv\n"
deps:
- path: 2021-usz-oropharynx/data.csv
hash: md5
md5: a9e4043ed6a273c609fa16523bcae455
size: 166966
- path: scripts/t_category.py
hash: md5
md5: 9cd603d2c51bbdb9b9c78f5d6c292914
size: 1647
plot-age-and-sex@2021-usz-oropharynx:
cmd: "python scripts/age_and_sex.py 2021-usz-oropharynx/data.csv\n"
deps:
- path: 2021-usz-oropharynx/data.csv
hash: md5
md5: a9e4043ed6a273c609fa16523bcae455
size: 166966
- path: scripts/age_and_sex.py
hash: md5
md5: e837a45727dd17cb4350ee4c1b1e5676
size: 3212
plot-subsite@2021-usz-oropharynx:
cmd: "python scripts/subsite.py --data 2021-usz-oropharynx/data.csv\n"
deps:
- path: 2021-usz-oropharynx/data.csv
hash: md5
md5: a9e4043ed6a273c609fa16523bcae455
size: 166966
- path: scripts/subsite.py
hash: md5
md5: 5f8736beb002a5fd9da22714a9129bf5
size: 4680
plot-subsite@2021-clb-oropharynx:
cmd: "python scripts/subsite.py --data 2021-clb-oropharynx/data.csv\n"
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/subsite.py
hash: md5
md5: 5f8736beb002a5fd9da22714a9129bf5
size: 4680
plot-subsite@2023-isb-multisite:
cmd: "python scripts/subsite.py --data 2023-isb-multisite/data.csv\n"
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/subsite.py
hash: md5
md5: 5f8736beb002a5fd9da22714a9129bf5
size: 4680
plot-subsite@2023-clb-multisite:
cmd: "python scripts/subsite.py --data 2023-clb-multisite/data.csv\n"
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 2ba19b79a80bf72f444dfe79a5165dc0
size: 113116
- path: scripts/subsite.py
hash: md5
md5: 5f8736beb002a5fd9da22714a9129bf5
size: 4680
bar-plot@2021-clb-oropharynx:
cmd: python scripts/bar_plot.py 2021-clb-oropharynx/data.csv
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/bar_plot.py
hash: md5
md5: 9d4f3f0c12f69d4bee3306c37d2f112c
size: 2585
bar-plot@2023-clb-multisite:
cmd: python scripts/bar_plot.py 2023-clb-multisite/data.csv
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 2ba19b79a80bf72f444dfe79a5165dc0
size: 113116
- path: scripts/bar_plot.py
hash: md5
md5: 9d4f3f0c12f69d4bee3306c37d2f112c
size: 2585
bar-plot@2023-isb-multisite:
cmd: python scripts/bar_plot.py 2023-isb-multisite/data.csv
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/bar_plot.py
hash: md5
md5: 9d4f3f0c12f69d4bee3306c37d2f112c
size: 2585
join:
cmd: "lyscripts data join --inputs 2021-clb-oropharynx/data.csv 2023-isb-multisite/data.csv
2023-clb-multisite/data.csv --output joined.csv\n"
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 2ba19b79a80bf72f444dfe79a5165dc0
size: 113116
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
outs:
- path: joined.csv
hash: md5
md5: ff3bb9aee56c1a154c48ff193e5081a5
size: 509532
enhance:
cmd: "lyscripts data enhance --consensus max_llh --params modalities.yaml joined.csv
enhanced.csv\n"
deps:
- path: joined.csv
hash: md5
md5: ff3bb9aee56c1a154c48ff193e5081a5
size: 509532
params:
modalities.yaml:
modalities:
CT:
- 0.76
- 0.81
MRI:
- 0.63
- 0.81
PET:
- 0.86
- 0.79
FNA:
- 0.98
- 0.8
diagnostic_consensus:
- 0.86
- 0.81
pathology:
- 1.0
- 1.0
pCT:
- 0.86
- 0.81
max_llh:
- 1.0
- 1.0
outs:
- path: enhanced.csv
hash: md5
md5: 2484477724436b9d1cc5f1a61434c093
size: 633424
scenario-showcase:
cmd: "python scripts/scenario_showcase.py --data enhanced.csv --mplstyle scripts/.mplstyle\n"
deps:
- path: enhanced.csv
hash: md5
md5: 2484477724436b9d1cc5f1a61434c093
size: 633424
- path: scripts/.mplstyle
hash: md5
md5: 1dd8e65e1d2705d5c02ec977b8e7ca0d
size: 2151
- path: scripts/scenario_showcase.py
hash: md5
md5: 1731456a8b37391a4c4ecaa7d939ebc6
size: 5104
outs:
- path: scenario_showcase.png
hash: md5
md5: c9327243c7afdcdb0c8c6bcd8a9d53b2
size: 86913