Copier

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.gitignore

@@ -1,12 +1,3 @@
-results/**
-resources/**
-logs/**
-.snakemake
-.snakemake/**
-.test/results/*
-workflow/notebooks/.ipynb_checkpoints/**
-**/.Rhistory
-**/*.Rproj
-**/.Rproj.user/**
-**/.RData
-**/Rplots.pdf
+# pixi environments
+.pixi/*
+!.pixi/config.toml

.test/config/config.yaml

@@ -1,8 +1 @@
-sample_sheet: "config/samples.tsv"
-
-get_genome:
-  ncbi_ftp: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz
-
-simulate_reads:
-  read_length: 100
-  read_number: 10000
+input_file: "data/input.txt"

copier.yml

@@ -0,0 +1,46 @@
+project_name:
+  type: str
+  help: What is your project name?
+
+features:
+  type: str
+  help: Which of these features are you interested in?
+  choices:
+    - isolated conda environments
+    - Jupyter Notebook Integration
+    - Report Generation
+    - Schema Validation
+
+# plugins:
+#   type: str
+#   help: Which of these features are you interested in?
+#   choices:
+#     - Schema Validation
+#     - Jupyter Notebook Integration
+#     - Report Generation
+#     -
+
+# scripts:
+#   type:
+#   help: What kind of scripts are you planning to use?
+#   choices:
+#     - notebooks
+#     - R
+#     - python
+#   multiselect: true
+
+# isolation:
+#   type:
+#   help: What container?
+#   choices:
+#     - pixi
+#     - conda
+#     - apptainer/singularity
+
+# profiles:
+#   type: boolean
+#   help: Would you like to set up a default profile?
+
+# orcid:
+#   type: boolean
+#   help: Would you like to link this workflow to an ORCID ID?

{{ project_name }}/.gitignore

@@ -0,0 +1,12 @@
+results/**
+resources/**
+logs/**
+.snakemake
+.snakemake/**
+.test/results/*
+workflow/notebooks/.ipynb_checkpoints/**
+**/.Rhistory
+**/*.Rproj
+**/.Rproj.user/**
+**/.RData
+**/Rplots.pdf

README.md → {{ project_name }}/README.md.jinja

@@ -1,13 +1,17 @@
-# Snakemake workflow: `<name>`
+# Snakemake workflow: `{{ project_name }}`
 
 [![Snakemake](https://img.shields.io/badge/snakemake-≥8.0.0-brightgreen.svg)](https://snakemake.github.io)
-[![GitHub actions status](https://github.com/<owner>/<repo>/workflows/Tests/badge.svg?branch=main)](https://github.com/<owner>/<repo>/actions?query=branch%3Amain+workflow%3ATests)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
-[![workflow catalog](https://img.shields.io/badge/Snakemake%20workflow%20catalog-darkgreen)](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/<owner>/<repo>)
 
-A Snakemake workflow for `<description>`
 
-- [Snakemake workflow: `<name>`](#snakemake-workflow-name)
+The workflow is built using [snakemake](https://snakemake.readthedocs.io/en/stable/) and consists of the following steps:
+
+1. Describe
+2. your
+3. rules
+4. here
+
+
+- [Snakemake workflow: `{{ project_name }}`](#snakemake-workflow-{{ project_name }})
   - [Usage](#usage)
   - [Deployment options](#deployment-options)
   - [Workflow profiles](#workflow-profiles)
@@ -17,8 +21,6 @@ A Snakemake workflow for `<description>`
 
 ## Usage
 
-The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/<owner>/<repo>).
-
 Detailed information about input data and workflow configuration can also be found in the [`config/README.md`](config/README.md).
 
 If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or its DOI.

config/README.md → {{ project_name }}/config/README.md

@@ -29,10 +29,5 @@ This table lists all parameters that can be used to run the workflow.
 
 | parameter          | type | details                               | default                        |
 | ------------------ | ---- | ------------------------------------- | ------------------------------ |
-| **sample_sheet**    |      |                                       |                                |
-| path               | str  | path to sample sheet, mandatory        | "config/samples.tsv"           |
-| **get_genome**     |      |                                       |                                |
-| ncbi_ftp           | str  | link to a genome on NCBI's FTP server | link to _S. cerevisiae_ genome |
 | **simulate_reads** |      |                                       |                                |
-| read_length        | num  | length of target reads in bp          | 100                            |
 | read_number        | num  | number of total reads to be simulated | 10000                          |

{{ project_name }}/data/config.yaml.jinja

@@ -0,0 +1,19 @@
+### GENERAL SNAKEMAKE SETTINGS
+
+# Tell snakemake which remote executor plugin to use, in our case the plugin
+# for the cluster system LSF, which is documented here:
+# https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/lsf.html
+# executor: "lsf"
+
+# Maximum number of cluster cores / cpus to schedule jobs for.
+#
+cores: { { max_cores } }
+
+# Always use conda environments for software deployment. Internally snakemake
+# implicitly uses mamba for speed (at the time of writing).
+software-deployment-method: { { sdm } }
+
+default-resources:
+  # The default amount of memory that is reserved for a rule, if the rule (and
+  # the snakemake command) don't specify anything else.
+  mem_mb: 4000

{{ project_name }}/data/input.txt

@@ -0,0 +1 @@
+Hello from Snakemake!

workflow/Snakefile → {{ project_name }}/workflow/Snakefile

@@ -8,23 +8,19 @@
 # -----------------------------------------------------
 configfile: "config/config.yaml"
 
-
 # load rules
 # -----------------------------------------------------
-include: "rules/common.smk"
-include: "rules/process_reads.smk"
+include: "rules/example.smk"
 
 
 # optional messages, log and error handling
 # -----------------------------------------------------
 onstart:
     print("\n--- Analysis started ---\n")
 
-
 onsuccess:
     print("\n--- Workflow finished! ---\n")
 
-
 onerror:
     print("\n--- An error occurred! ---\n")
 
@@ -33,5 +29,5 @@ onerror:
 # -----------------------------------------------------
 rule all:
     input:
-        "results/multiqc/multiqc_report.html",
+        "results/output.txt"
     default_target: True