finish up readme

README.md

@@ -1,21 +1,21 @@
-# Snakemake workflow: `<name>`
+# Snakemake workflow: `<snakemake_template>`
 
-[![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)
+[![Snakemake](https://img.shields.io/badge/snakemake-≥7.18.2-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)
 
+This is a template repository designed for scientific projects where data is processed using [Snakemake](https://snakemake.readthedocs.io/).
 
-A Snakemake workflow for `<description>`
-
+## Requirements
+All required tools are automatically installed by Snakemake using conda environments or singularity/apptainer containers, however Snakemake itself needs to be installed first. Load a software module with Snakemake, use a native install, or use the `environment.yml` file to create a conda environment for this particular project using fx `mamba env create -n <snakemake_template> -f environment.yml`.
 
 ## Usage
-
-The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=<owner>%2F<repo>).
-
-If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) <repo>sitory and its DOI (see above).
+Adjust the `config.yaml` files under both `config/` and `profiles/` accordingly, then simply run `snakemake --profile profiles/<subfolder>` or submit a SLURM job using the `slurm_submit.sbatch` example script.
+The usage of this workflow is also described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=<owner>%2F<repo>).
 
 # TODO
-
-* Replace `<owner>` and `<repo>` everywhere in the template (also under .github/workflows) with the correct `<repo>` name and owning user or organization.
-* Replace `<name>` with the workflow name (can be the same as `<repo>`).
-* Replace `<description>` with a description of what the workflow does.
-* The workflow will occur in the snakemake-workflow-catalog once it has been made public. Then the link under "Usage" will point to the usage instructions if `<owner>` and `<repo>` were correctly set.
+* Replace `<owner>` and `<repo>` with the correct values in this `README.md` as well as in files under `.github/workflows/`.
+* Replace `<snakemake_template>` with the workflow/project name (can be the same as `<repo>`) here as well as in the `environment.yml` and `slurm_submit.sbatch` files.
+* Add more requirements to the `environment.yml` file if needed, however tools for each Snakemake rule should **NOT** go here, they should be configured separately for each rule instead in `yaml` files under `envs/`.
+* Fill in fields in this `README.md` file, in particular provide a proper description of what the workflow does with any relevant details and configuration.
+* The workflow will occur in the public Snakemake workflow catalog once the repository has been made public and the provided GitHub actions finish correctly. Then the link under "Usage" will point to the usage instructions if `<owner>` and `<repo>` were correctly set.
+* DELETE this **TODO** section when finished with all of the above.

environment.yml

@@ -1,4 +1,4 @@
-name: snakemake_template
+name: <snakemake_template>
 channels:
   - bioconda
   - conda-forge

profiles/biocloud/config.yaml

@@ -1,4 +1,4 @@
-#command with which to start SLURM jobs
+#command with which to submit rules as SLURM jobs
 cluster:
   mkdir -p logs/{rule}/ &&
   sbatch
@@ -31,4 +31,5 @@ rerun-incomplete: True
 scheduler: greedy
 max-status-checks-per-second: 5
 cluster-cancel: scancel
-cluster-status: extras/slurm-status.sh #script to get job status for snakemake
+#script to get job status for snakemake, unfortunately neccessary
+cluster-status: extras/slurm-status.sh

slurm_submit.sbatch

@@ -1,5 +1,5 @@
 #!/usr/bin/bash -l
-#SBATCH --job-name=snakemake_template
+#SBATCH --job-name=<snakemake_template>
 #SBATCH --output=job_%j_%x.out
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
@@ -14,7 +14,7 @@
 set -eu
 
 # Activate conda environment with only snakemake
-conda activate snakemake_template
+conda activate <snakemake_template>
 
 # Start workflow using ressources defined in the profile. Snakemake itself 
 # requires nothing, 1CPU + 1G mem is enough
@@ -23,7 +23,7 @@ conda activate snakemake_template
 snakemake --dag | dot -Tsvg > results/dag.svg
 
 # Main workflow
-snakemake --forceall --profile profiles/biocloud
+snakemake --profile profiles/biocloud
 
 # Optionally generate a report once finished
 snakemake --report results/report.html