Add changes

Author: github-actions[bot]

data.json

@@ -92197,28 +92197,6 @@
     "topics": [],
     "updated_at": 1617236099.0
   },
-  {
-    "config_readme": null,
-    "data_format": 2,
-    "description": null,
-    "formatting": null,
-    "full_name": "tucca-cellag/PNPDP",
-    "latest_release": null,
-    "linting": null,
-    "mandatory_flags": [],
-    "non_standardized_reason": [
-      "no .snakemake-workflow-catalog.yml found in repo root",
-      "no config/README.md found in repo root"
-    ],
-    "report": false,
-    "software_stack_deployment": null,
-    "standardized": false,
-    "stargazers_count": 1,
-    "subscribers_count": 0,
-    "topics": [],
-    "updated_at": 1761083017.0,
-    "wrappers": {}
-  },
   {
     "config_readme": "## Disclaimer (Workflow Under-Construction)\n\n**THIS REPO IS STILL UNDER CONSTRUCTION AND DOES NOT REPRESENT A COMPLETED WORKFLOW**\n\nIn the meantime, feel free to [contact the current maintainer](mailto:benjamin.bromberg@tufts.edu)\nwith any questions.\n\nTo configure the workflow please refer to the official documentation for\n`tucca-rna-seq`, which can be found\n[here](https://tucca-cellag.github.io/tucca-rna-seq/introduction).",
     "data_format": 2,
@@ -98044,28 +98022,6 @@
     "topics": [],
     "updated_at": 1724838425.0
   },
-  {
-    "config_readme": null,
-    "data_format": 2,
-    "description": null,
-    "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpucw3o_n3/Snakefile\":  Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.11.4",
-    "full_name": "zlewkarzbenc/ztp4",
-    "latest_release": null,
-    "linting": "Lints for rule pm25_metrics (line 9, /tmp/tmpucw3o_n3/Snakefile):\n    * No log directive defined:\n      Without a log directive, all output will be printed to the terminal. In\n      distributed environments, this means that errors are harder to discover.\n      In local environments, output of concurrent jobs will be mixed and become\n      unreadable.\n      Also see:\n      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n    * Specify a conda environment or container for each rule.:\n      This way, the used software for each specific step is documented, and the\n      workflow can be executed on any machine without prerequisites.\n      Also see:\n      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule pubmed_fetch (line 28, /tmp/tmpucw3o_n3/Snakefile):\n    * No log directive defined:\n      Without a log directive, all output will be printed to the terminal. In\n      distributed environments, this means that errors are harder to discover.\n      In local environments, output of concurrent jobs will be mixed and become\n      unreadable.\n      Also see:\n      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n    * Specify a conda environment or container for each rule.:\n      This way, the used software for each specific step is documented, and the\n      workflow can be executed on any machine without prerequisites.\n      Also see:\n      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule report (line 42, /tmp/tmpucw3o_n3/Snakefile):\n    * No log directive defined:\n      Without a log directive, all output will be printed to the terminal. In\n      distributed environments, this means that errors are harder to discover.\n      In local environments, output of concurrent jobs will be mixed and become\n      unreadable.\n      Also see:\n      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n    * Specify a conda environment or container for each rule.:\n      This way, the used software for each specific step is documented, and the\n      workflow can be executed on any machine without prerequisites.\n      Also see:\n      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n",
-    "mandatory_flags": [],
-    "non_standardized_reason": [
-      "no .snakemake-workflow-catalog.yml found in repo root",
-      "no config/README.md found in repo root"
-    ],
-    "report": false,
-    "software_stack_deployment": null,
-    "standardized": false,
-    "stargazers_count": 0,
-    "subscribers_count": 0,
-    "topics": [],
-    "updated_at": 1771594247.0,
-    "wrappers": {}
-  },
   {
     "config_readme": null,
     "data_format": 2,

skips.json

@@ -16867,10 +16867,6 @@
     "full_name": "sylvainschmitt/troll_tee",
     "updated_at": 1758183178.0
   },
-  {
-    "full_name": "sylvestermoyo-z/umoja",
-    "updated_at": 1759292409.0
-  },
   {
     "full_name": "sysbiolux/DeepOncoAI",
     "updated_at": 1730714998.0
@@ -17391,10 +17387,6 @@
     "full_name": "tyongo/rnaseq-differential-expression-pipeline",
     "updated_at": 1768948564.0
   },
-  {
-    "full_name": "tyydorothy/python-basics",
-    "updated_at": 1769074607.0
-  },
   {
     "full_name": "tzhang-nmdp/CYTO-SV-ML",
     "updated_at": 1736792597.0
@@ -18351,10 +18343,6 @@
     "full_name": "zl3327/Immune-Nets-Snakemake-Pipeline",
     "updated_at": 1730823959.0
   },
-  {
-    "full_name": "zlewkarzbenc/klasyfikator",
-    "updated_at": 1771802725.0
-  },
   {
     "full_name": "zm-git-dev/my_binder",
     "updated_at": 1660378779.0