add troubleshooting page

docs/1-troubleshooting.md

@@ -0,0 +1,42 @@
+# Troubleshooting
+
+## Creating a new Snakemake profile
+
+
+!!! screwdriver-wrench "Create a new Snakemake profile with cookiecutter"
+
+    * Load a `snakemake` module Or make sure `snakemake` in `$PATH`
+
+
+    1. If not already, create a configuration directory for Snakemake profiles:
+
+        ```bash
+        profile_dir="${HOME}/.config/snakemake"
+        mkdir -p "$profile_dir"
+        ```
+
+    2.  Use `cookiecutter` to create the Slurm profile template:
+        - If `cookiecutter` isn't installed, load snakemake module and run `pip install --user cookiecutter`
+            ```bash
+            template="gh:Snakemake-Profiles/slurm"
+            cookiecutter --output-dir "$profile_dir" "$template"
+            ```
+
+    3. During the cookiecutter process, you'll be prompted to set values for your profile. For example:
+        ```bash
+        profile_name [slurm]: myprofile
+        sbatch_defaults []: account=my_account no-requeue exclusive
+        cluster_sidecar_help: [Use cluster sidecar. NB! Requires snakemake >= 7.0! Enter to continue...]
+        Select cluster_sidecar:
+        1 - yes
+        2 - no
+        Choose from 1, 2 :
+        cluster_name []:
+        ```
+    4. After completing the prompts, the profile scripts and configuration file will be installed in the $profile_dir ( `~/.config/snakemake`).
+
+    5. You can then use this profile when running Snakemake by calling it via  `--profile` flag:
+
+        ```python
+        snakemake --profile myprofile ...
+        ```