diff --git a/workflow/scripts/delete_entry.py b/workflow/scripts/delete_entry.py index 1b26509a8c1541f65a39e660ec7e6ec158194ef1..77207e810e518ceca3888be8f14793f9891317db 100644 --- a/workflow/scripts/delete_entry.py +++ b/workflow/scripts/delete_entry.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#delete_entry.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -34,4 +42,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credentials = {"cookie": args.cookie} - main(host, 2, credentials) \ No newline at end of file + main(host, 2, credentials) diff --git a/workflow/scripts/extract_ref_data.py b/workflow/scripts/extract_ref_data.py index bf06c95696354e6fe5d445718fbfb0769df4182d..87fc1e06ba0e50cac61ade8232d3330998ac9d42 100644 --- a/workflow/scripts/extract_ref_data.py +++ b/workflow/scripts/extract_ref_data.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#extract_ref_data.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import argparse import pandas as pd diff --git a/workflow/scripts/generate_references.py b/workflow/scripts/generate_references.py index 8e809f1e4471d3393ec4960778d2a210d54c11d1..d72b3522aa1963475b103d32a4087052402edca8 100644 --- a/workflow/scripts/generate_references.py +++ b/workflow/scripts/generate_references.py @@ -2,7 +2,7 @@ #generate_references.py #* #* -------------------------------------------------------------------------- -#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE) +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) #* -------------------------------------------------------------------------- #* diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py index 2ff498659cc9acbf989ec45e61e8b755b9cc3a66..1ee16837731d88654be0f099a6a4aca9e3264c09 100644 --- a/workflow/scripts/generate_versions.py +++ b/workflow/scripts/generate_versions.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# -*- coding: utf-8 -*- - -# -# * -------------------------------------------------------------------------- -# * Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/master/LICENSE) -# * -------------------------------------------------------------------------- -# +#generate_versions.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* '''Make YAML of software versions.''' diff --git a/workflow/scripts/parse_meta.py b/workflow/scripts/parse_meta.py index 52f0f18200525f776fe73fcf2f4cd5be8db35045..64f9e559d6768127889055d59b23cc303fcb4e92 100644 --- a/workflow/scripts/parse_meta.py +++ b/workflow/scripts/parse_meta.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#parse_meta.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import argparse import pandas as pd diff --git a/workflow/scripts/tin_hist.py b/workflow/scripts/tin_hist.py index ee36bb6447dfe0adcdaab60e1224cca5b5a6e246..599f285120911770332034e5ace1dd211c51ecd4 100644 --- a/workflow/scripts/tin_hist.py +++ b/workflow/scripts/tin_hist.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#tin_hist.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import argparse import pandas as pd diff --git a/workflow/scripts/upload_execution_run.py b/workflow/scripts/upload_execution_run.py index 405c81aa9c2aa31c500157bee3db39413789a7fa..5fd0cf4a35bdd8b107261e18472c55de48886ae8 100644 --- a/workflow/scripts/upload_execution_run.py +++ b/workflow/scripts/upload_execution_run.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_execution_run.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -58,4 +66,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credentials = {"cookie": args.cookie} - main(host, 2, credentials) \ No newline at end of file + main(host, 2, credentials) diff --git a/workflow/scripts/upload_input_bag.py b/workflow/scripts/upload_input_bag.py index ab4d338074ffec3098667dcf2817041e01ded8bd..434129d2a821b59aab99c94bc618a8424c4c8196 100644 --- a/workflow/scripts/upload_input_bag.py +++ b/workflow/scripts/upload_input_bag.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_input_bag.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -43,4 +51,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credential = {"cookie": args.cookie} - main(host, 2, credential) \ No newline at end of file + main(host, 2, credential) diff --git a/workflow/scripts/upload_output_bag.py b/workflow/scripts/upload_output_bag.py index e1e1fc1a7fc59e2b003f3c6602f06182c9a3b054..a4ac6307c194d65f4729a0f37ff380eba1c57e65 100644 --- a/workflow/scripts/upload_output_bag.py +++ b/workflow/scripts/upload_output_bag.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_output_bag.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -54,4 +62,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credential = {"cookie": args.cookie} - main(host, 2, credential) \ No newline at end of file + main(host, 2, credential) diff --git a/workflow/scripts/upload_qc.py b/workflow/scripts/upload_qc.py index 29fac063d9812ad05877d3e8f8f0d865d52eca14..3c51bc8902a0dbd6a7b64ca0cdaef056b18020c4 100644 --- a/workflow/scripts/upload_qc.py +++ b/workflow/scripts/upload_qc.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_qc.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -72,4 +80,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credentials = {"cookie": args.cookie} - main(host, 2, credentials) \ No newline at end of file + main(host, 2, credentials) diff --git a/workflow/scripts/utils.py b/workflow/scripts/utils.py index 548b84c0642ee1479c1ac2e968ba1cd1aa9ed660..dc49b345661edf88964a3c3eb491e3f9e17feed9 100644 --- a/workflow/scripts/utils.py +++ b/workflow/scripts/utils.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#utils.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import shlex import logging