Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

cleanup old files #69

Merged
merged 8 commits into from
Sep 9, 2022
Merged

cleanup old files #69

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
8d3edaa
rm outdated lists
raynamharris Sep 8, 2022
92fd8d3
rm outdated lists
raynamharris Sep 8, 2022
abfba3e
rename input list
raynamharris Sep 8, 2022
ac9cad2
consistent input names
raynamharris Sep 8, 2022
aa69630
update input files
raynamharris Sep 8, 2022
bd29da6
better names
raynamharris Sep 8, 2022
8902133
better names
raynamharris Sep 8, 2022
5196193
Merge branch 'main' into cleanup
raynamharris Sep 9, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions Snakefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,7 @@ rule gene_json_alias_widget:
message: "build alias widgets for genes"
input:
script = "scripts/build-markdown-pieces-gene-translate.py",
id_list = "data/inputs/STAGING_PORTAL__available_genes__2022-08-19.txt",
id_list = "data/inputs/gene_IDs_for_alias_tables.txt",
alias_info = "data/inputs/Homo_sapiens.gene_info_20220304.txt_conv_wNCBI_AC.txt",
output:
directory("output_pieces_gene/00-alias")
Expand All @@ -140,7 +140,7 @@ rule gene_json_appyter_link:
message: "build gene/appyter links for genes"
input:
script = "scripts/build-appyter-gene-links.py",
id_list = "data/inputs/STAGING_PORTAL__available_genes__2022-08-19.txt",
id_list = "data/inputs/gene_IDs_for_alias_tables.txt",
output:
directory("output_pieces_gene/01-appyter")
params:
Expand Down Expand Up @@ -234,7 +234,7 @@ rule anatomy_link:
message: "add link to embl ols"
input:
script = "scripts/build-anatomy-links.py",
id_list = "data/inputs/STAGING_PORTAL__anatomy__2022-07-22.txt",
id_list = "data/inputs/anatomy_IDs_for_embl.txt",
output:
directory("output_pieces_anatomy/01-embl")
params:
Expand All @@ -249,7 +249,7 @@ rule anatomy_json_expression_widget:
message: "build expression widgets for anatomy terms"
input:
script = "scripts/build-markdown-pieces.py",
id_list = "data/inputs/anatomy_gtex.txt",
id_list = "data/inputs/anatomy_IDs_for_gtex.txt",
output:
directory("output_pieces_anatomy/10-expression")
params:
Expand Down Expand Up @@ -411,7 +411,7 @@ rule protein_json_disease:
message: "build protein markdown for diseases"
input:
script = "scripts/build-protein-disease.py",
id_list = "data/inputs/proteins_IDs_withdisease.txt",
id_list = "data/inputs/protein_IDs_for_disease.txt",
disease_name_file = "data/inputs/disease_names.txt",
alias_info = "data/inputs/protein2disease.txt",
output:
Expand Down Expand Up @@ -447,7 +447,7 @@ rule disease_json_links:
message: "build links for disease terms"
input:
script = "scripts/build-disease-links.py",
id_list = "data/inputs/test/disease_IDs.txt",
id_list = "data/inputs/disease_IDs.txt",
output:
directory("output_pieces_disease/00-links")
params:
Expand Down
691 changes: 0 additions & 691 deletions data/inputs/Anatomy.csv
View file
Open in desktop

This file was deleted.

Loading