add docker, still experimental

README.md

@@ -46,7 +46,20 @@ snakemake --jobs 24 --slurm \
   --rerun-incomplete --retries 3 \
   --use-envmodules --latency-wait 10 \
   --default-resources slurm_account=kawahara slurm_partition=hpg-milan
+```
+
+</details>
+
+<details>
+  <summary>Run with Docker:</summary>
+
+Say, in 'the cloud' using [FlowDeploy](https://flowdeploy.com/).
 
+```bash
+snakemake --jobs 12 \
+  --rerun-incomplete --retries 3 \
+  --use-singularity \
+  --default-resources
 ```
 
 </details>

config/config.yaml

@@ -1,12 +1,16 @@
-# Qiime2 version number
+# Qiime2 target version number
 q2v: "2023.9"
+
+# Software setup:
 # Qiime2 conda environment
 # Get full file from from https://github.com/qiime2/environment-files
 q2env: "envs/qiime2-amplicon-2023.9-py38-linux-conda.yml"
 # Or specify name of already installed Qiime2 environment
 # q2env: "qiime2-amplicon-2023.9"
 # Or load a pre-installed module
 q2mod: "qiime2/2023.9"
+# Or pull a pre-built docker container
+q2docker: "docker://quay.io/qiime2/amplicon:2023.9"
 
 # UNITE Major version listed in file names
 version: "ver9"

workflow/Snakefile

@@ -8,8 +8,10 @@ from snakemake.io import glob_wildcards, expand
 
 configfile: "config/config.yaml"
 
+
 include: "common.smk"  # python helper functions
 
+
 # Prevents the 'download' rule from running on worker nodes
 localrules:
     all,
@@ -19,6 +21,7 @@ localrules:
 # load and set conda envs and modules from the config
 Q2CONDA = config["q2env"]
 Q2MOD = config["q2mod"]
+Q2DOCKER = config["q2docker"]
 
 GOALS = expand(
     "results/unite_{ver}_{id}_{type}{date}-Q2-{q2v}.qza",
@@ -86,6 +89,8 @@ rule import_seqs:
         Q2CONDA
     envmodules:
         Q2MOD,
+    container:
+        Q2DOCKER
     shell:
         """
         qiime tools import \
@@ -107,6 +112,8 @@ rule import_tax:
         Q2CONDA
     envmodules:
         Q2MOD,
+    container:
+        Q2DOCKER
     shell:
         """
         qiime tools import \
@@ -129,10 +136,12 @@ rule train:
         Q2CONDA
     envmodules:
         Q2MOD,
+    container:
+        Q2DOCKER
     benchmark:
         "logs/train_{ver}_{id}_{type}{date}-Q2-{q2v}.tsv"
     resources:
-        mem_mb=get_mem_mb,  # see function above
+        mem_mb=get_mem_mb,  # see common.smk
         runtime="24h",  # hopefully not
     shell:
         """