- "linting": "Lints for snakefile /tmp/tmpj4xyi9ag/shahab-ab-project-g3-552b562/workflow/rules/unpack_sample.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n 'rules/common.smk'. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule pick_lineage (line 31, /tmp/tmpj4xyi9ag/shahab-ab-project-g3-552b562/workflow/rules/assign_lineage.smk):\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 copy_genome (line 1, /tmp/tmpj4xyi9ag/shahab-ab-project-g3-552b562/workflow/rules/prepare_genome.smk):\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 correct_denovo (line 1, /tmp/tmpj4xyi9ag/shahab-ab-project-g3-552b562/workflow/rules/de_novo/02_scaffold.smk):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule scaffold_denovo (line 33, /tmp/tmpj4xyi9ag/shahab-ab-project-g3-552b562/workflow/rules/de_novo/02_scaffold.smk):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule patch_denovo (line 65, /tmp/tmpj4xyi9ag/shahab-ab-project-g3-552b562/workflow/rules/de_novo/02_scaffold.smk):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n",
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