Merge pull request #36 from mrvollger/smk8

Update to snakemake v8

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
@@ -105,15 +105,15 @@ 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.
 
 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:

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"
 
 

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