diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index ef21205..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,60 +0,0 @@
-FROM condaforge/mambaforge:latest
-LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="fd0eeef546ed00fa95ff85a8baf143dfccd52a6183b57e9bb8e972bf196948d5"
-
-# Step 1: Retrieve conda environments
-
-# Conda environment:
-#   source: workflow/envs/R.yaml
-#   prefix: /conda-envs/ee4bfa88159ef77575445596ec2221ce
-#   name: R
-#   channels:
-#     - conda-forge
-#     - r
-#     - defaults
-#   dependencies:
-#     #- xorg-libx11
-#     #- xorg-libxau
-#     #- r::r-ggplot2
-#     - r-base>=4.0
-#     - r-essentials
-#     - r-cairo
-#     - r-data.table
-#     - r-cowplot
-#     - r-argparse>=2.1.2
-#     - r-glue
-#     - r-r.utils
-#     - r-rcolorbrewer
-#     - r-scales
-#     - r-tidyverse>=1.3.0
-RUN mkdir -p /conda-envs/ee4bfa88159ef77575445596ec2221ce
-COPY workflow/envs/R.yaml /conda-envs/ee4bfa88159ef77575445596ec2221ce/environment.yaml
-
-# Conda environment:
-#   source: workflow/envs/env.yaml
-#   prefix: /conda-envs/5ea0207c595d8a051ab13a13766b14f6
-#   name: python_and_cli_env
-#   channels:
-#     - conda-forge
-#     - bioconda
-#     - defaults
-#   dependencies:
-#     - numpy<1.20
-#     - numba
-#     - cooler<=0.8.11
-#     - pandas<=1.5
-#     - minimap2==2.18
-#     - bioconda::bedtools
-#     - bioconda::samtools>=1.14
-#     - bioconda::htslib>=1.14
-#     - bioconda::pysam>=0.15.0
-#     - bioconda::bwa
-#     - pigz
-RUN mkdir -p /conda-envs/5ea0207c595d8a051ab13a13766b14f6
-COPY workflow/envs/env.yaml /conda-envs/5ea0207c595d8a051ab13a13766b14f6/environment.yaml
-
-# Step 2: Generate conda environments
-
-RUN mamba env create --prefix /conda-envs/ee4bfa88159ef77575445596ec2221ce --file /conda-envs/ee4bfa88159ef77575445596ec2221ce/environment.yaml && \
-    mamba env create --prefix /conda-envs/5ea0207c595d8a051ab13a13766b14f6 --file /conda-envs/5ea0207c595d8a051ab13a13766b14f6/environment.yaml && \
-    mamba clean --all -y
diff --git a/README.md b/README.md
index 0e92443..3a46e03 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ To install you can follow the directions on the [usage page](https://snakemake.g
 You will need a current version of `snakemake` to run this workflow. To get `snakemake` please follow the install [instructions](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) on their website, but in brief once `conda` and `mamba` are installed you can install `snakemake` with:
 
 ```
-mamba create -n snakemake -c conda-forge -c bioconda snakemake
+mamba create -n snakemake -c conda-forge -c bioconda 'snakemake>=8'
 ```
 
 Afterwards you can activate the `conda` environment and download the repository. And all additional dependencies will be handled by `snakemake`.
@@ -31,20 +31,20 @@ Choose a sample identifier for your run e.g. `chr8` and a fasta file on which yo
 Once this is done and you have activated your `conda` env with `snakemake` you can run the pipeline like so:
 
 ```
-snakemake --use-conda --cores 24
+snakemake --cores 24
 ```
 
 Or do a dry run of the pipeline:
 
 ```
-snakemake --use-conda --cores 24 -n
+snakemake --cores 24 -n
 ```
 
 All parameters are described in `config/README.md` and you can modify any of them
 by modifying `config/config.yaml`. You can also change the configuration via the command line. For example, to change the `sample` identifier and `fasta` options do:
 
 ```
-snakemake --use-conda --cores 24 --config sample=test2 fasta=/some/fasta/path.fa
+snakemake --cores 24 --config sample=test2 fasta=/some/fasta/path.fa
 ```
 
 Please try the test case with the default configuration file before submitting issues.
@@ -59,7 +59,7 @@ The file `results/{sample}.{\d+}.{\d+}.bed` will contain all the alignments iden
 To make pdfs and pngs for a particular set of regions just add `make_figures` to your command. This is generally appropriate for comparing up to ~5 regions totaling at most ~40 Mbp.
 
 ```
-snakemake --use-conda --cores 24 make_figures
+snakemake --cores 24 make_figures
 ```
 
 This will make an output directory under `results/{sample}.{\d+}.{\d+}_figures` with a variety of dot plots in `pdf` and `png` format.
@@ -71,7 +71,7 @@ If you see `tri.TRUE` in the output pdf/png it means that the dot plot is rotate
 Making an interactive whole genome visualization requires the use of the program [HiGlass](https://higlass.io/) and a web browser. However, this pipeline will make the necessary input files with the following command:
 
 ```
-snakemake --use-conda --cores 24 cooler
+snakemake --cores 24 cooler
 ```
 
 To view locally, use `higlass-manage`:
@@ -89,7 +89,7 @@ To create a high-resolution interactive visualization where the
 coloring is proportionally to the number of reads mapped to each bin, use the following command:
 
 ```
-snakemake --use-conda --cores 24 cooler_density --config window=32 cooler_window=100
+snakemake --cores 24 cooler_density --config window=32 cooler_window=100
 ```
 
 ## Arabidopsis: quick start, case example, and benchmark
@@ -105,7 +105,7 @@ wget https://github.com/schatzlab/Col-CEN/raw/main/v1.2/Col-CEN_v1.2.fasta.gz \
 Using 8 cores on a laptop with 32 GB of ram we ran StainedGlass using the following commands:
 
 ```shell
-time snakemake --cores 8 --config sample=arabidopsis fasta=Col-CEN_v1.2.fasta --use-conda
+time snakemake --cores 8 --config sample=arabidopsis fasta=Col-CEN_v1.2.fasta
 ```
 
 This command generated 41,036,963 self-self pairwise alignments within the assembly, 16,699,976 of which passed filters for downstream analysis.
@@ -113,7 +113,7 @@ This command generated 41,036,963 self-self pairwise alignments within the assem
 Then to generate the cooler files that can be loaded in HiGlass we ran the following command with the already computed alignments:
 
 ```shell
-time snakemake --cores 8 --config sample=arabidopsis fasta=Col-CEN_v1.2.fasta --use-conda cooler
+time snakemake --cores 8 --config sample=arabidopsis fasta=Col-CEN_v1.2.fasta cooler
 ```
 
 The results can be viewed at [resgen.io/paper-data/Naish](https://resgen.io/paper-data/Naish%202021%20-%20Arabidopsis/views/EYd0Kq5XTY6jhKpCK08Jjg/), and we include a static view of the centromeres here:
diff --git a/workflow/Snakefile b/workflow/Snakefile
index ad167b1..0b25538 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -4,7 +4,7 @@ import sys
 
 from snakemake.utils import min_version
 
-min_version("6.0")
+min_version("8.0")
 
 bold = "\033[1m"
 green = "\033[92m"
@@ -18,10 +18,12 @@ msg = f"""{green}{bold}Thanks for using StainedGlass and please remember to cite
 """
 sys.stderr.write(msg)
 
-SDIR = os.path.realpath(os.path.dirname(srcdir("Snakefile")))
 shell.prefix(f"set -eo pipefail; ")
 
 
+# container: "docker://continuumio/miniconda3"
+
+
 configfile: "config/config.yaml"
 
 
diff --git a/workflow/profiles/default/config.yaml b/workflow/profiles/default/config.yaml
new file mode 100644
index 0000000..3edfd55
--- /dev/null
+++ b/workflow/profiles/default/config.yaml
@@ -0,0 +1,10 @@
+default-resources:
+  - mem_mb=16096
+  - runtime=120
+rerun-incomplete: True
+rerun-triggers: mtime
+use-conda: True
+#use-singularity: True
+show-failed-logs: True
+conda-frontend: conda
+cores: 4