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Author: github-actions[bot]

data.json

@@ -80510,23 +80510,6 @@
     "updated_at": 1774537918.0,
     "wrappers": {}
   },
-  {
-    "config_readme": null,
-    "data_format": 2,
-    "description": "Automated version of APPSquared Pipeline plus updates",
-    "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp2a60vgqm/Snakefile\":  Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2",
-    "full_name": "nicolepaterson/Automated_APPSquared_2_0",
-    "latest_release": null,
-    "linting": "WorkflowError in file /tmp/tmp2a60vgqm/Snakefile, line 1:\nConfig file must be given as JSON or YAML with keys at top level.\n",
-    "mandatory_flags": [],
-    "report": false,
-    "software_stack_deployment": null,
-    "standardized": false,
-    "stargazers_count": 0,
-    "subscribers_count": 1,
-    "topics": [],
-    "updated_at": 1738954288.0
-  },
   {
     "config_readme": "## Workflow overview\n\nThis workflow is a best-practice workflow for `<detailed description>`.\nThe workflow is built using [snakemake](https://snakemake.readthedocs.io/en/stable/) and consists of the following steps:\n\n1. Download genome reference from NCBI\n2. Validate downloaded genome (`python` script)\n3. Simulate short read sequencing data on the fly (`dwgsim`)\n4. Check quality of input read data (`FastQC`)\n5. Collect statistics from tool output (`MultiQC`)\n\n## Running the workflow\n\n### Input data\n\nThis template workflow creates artificial sequencing data in `*.fastq.gz` format.\nIt does not contain actual input data.\nThe simulated input files are nevertheless created based on a mandatory table linked in the `config.yaml` file (default: `.test/samples.tsv`).\nThe sample sheet has the following layout:\n\n| sample  | condition | replicate | read1                      | read2                      |\n| ------- | --------- | --------- | -------------------------- | -------------------------- |\n| sample1 | wild_type | 1         | sample1.bwa.read1.fastq.gz | sample1.bwa.read2.fastq.gz |\n| sample2 | wild_type | 2         | sample2.bwa.read1.fastq.gz | sample2.bwa.read2.fastq.gz |\n\n### Parameters\n\nThis table lists all parameters that can be used to run the workflow.\n\n| parameter          | type | details                               | default                        |\n| ------------------ | ---- | ------------------------------------- | ------------------------------ |\n| **sample_sheet**    |      |                                       |                                |\n| path               | str  | path to sample sheet, mandatory        | \"config/samples.tsv\"           |\n| **get_genome**     |      |                                       |                                |\n| ncbi_ftp           | str  | link to a genome on NCBI's FTP server | link to _S. cerevisiae_ genome |\n| **simulate_reads** |      |                                       |                                |\n| read_length        | num  | length of target reads in bp          | 100                            |\n| read_number        | num  | number of total reads to be simulated | 10000                          |\n",
     "data_format": 3,
@@ -82088,30 +82071,6 @@
     "updated_at": 1763918506.0,
     "wrappers": {}
   },
-  {
-    "config_readme": null,
-    "data_format": 3,
-    "description": "Snakemake workflow to get mitochondrial genomes from metagenomic data",
-    "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/tree.2.alignment.smk\":  Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/tree.1.mitos.smk\":  Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/0.preflight.smk\":  InvalidPython: Black error:\n```\nCannot parse for target version Python 3.13: 2:0:     if os.path.isdir(dir[\"log\"]):\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/0.preflight.smk\":  \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/search.2.mappingGene.smk\":  Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/search.2.mapping-search.smk\":  Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/tree.3.genetrees.smk\":  Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/QC-reports.smk\":  Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/1.qc.smk\":  Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/3.Mitogenomes.smk\":  NoParametersError: L235: In params definition.\n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/3.Mitogenomes.smk\":  \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/Mitogenome-reports.smk\":  Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/Snakefile\":  InvalidPython: Black error:\n```\nCannot parse for target version Python 3.13: 37:0: <line number missing in source>\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/Snakefile\":  \n[DEBUG] In file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/2.mapping.smk\":  Formatted content is different from original\n[INFO] 3 file(s) raised parsing errors \ud83e\udd15\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.11.4",
-    "full_name": "npbhavya/MitoBee",
-    "latest_release": "v1.0",
-    "linting": "TypeError in file \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/0.preflight.smk\", line 55:\nexpected str, bytes or os.PathLike object, not NoneType\n  File \"/tmp/tmpihn1o5_4/npbhavya-MitoBee-7609bb3/workflow/rules/0.preflight.smk\", line 55, in <module>\n  File \"<frozen posixpath>\", line 76, in join\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,
-    "rulegraph": null,
-    "schemas": null,
-    "software_stack_deployment": null,
-    "standardized": false,
-    "stargazers_count": 0,
-    "subscribers_count": 0,
-    "topics": [],
-    "updated_at": 1773654004.0,
-    "wrappers": {}
-  },
   {
     "config_readme": null,
     "data_format": 2,

skips.json

@@ -13991,10 +13991,6 @@
     "full_name": "mrvollger/assembly_workflows",
     "updated_at": 1637289973.0
   },
-  {
-    "full_name": "mschecht/cellranger-snakemake",
-    "updated_at": 1773444186.0
-  },
   {
     "full_name": "mschubert/R-hpc",
     "updated_at": 1647455149.0