Update and pin dependencies

README.md

@@ -68,7 +68,7 @@ Replace the YAML keys as appropriate. Keys are:
 | `slack_token` | str, optional | if you want to be bombarded with slack messages regarding the success and failure of your snakes, insert a suitable bot API token here |
 | `slack_channel` | str, optional | if using a `slack_token`, enter the name of the channel to send messages, including the leading `#` |
 | `cuda` | boolean | set to `False` if you do not want GPU-acceleration and `True` if you have the means to go very fast (*i.e.* you have a CUDA-compatible GPU) |
-| `medaka_env` | URI | path to a singularity image (simg) or sandbox container to run medaka (CPU or GPU) |
+| `medaka_env` | URI | path to a singularity image (simg) or sandbox container to run medaka (GPU only as conda env will interfere with simg on CPU mode) |
 | `racon_batches`| int | number of simultaneous batches to process on GPU |
 | `polish_threads` | int | number of CPU threads to use for any polishing step |
 | `polish_gpu` | int | number of GPU devices to use for any on-GPU polishing step |
@@ -169,6 +169,10 @@ For a full invocation example:
 snakemake -j <available_threads> --reason --use-conda --use-singularity --singularity-args '--nv -B <dir_inside>:<dir_outside>' -k --restart-times 1 --resources gpu=N
 ```
 
+## Notes
+
+* Reticulatus is currently pinned to `medaka v0.11.5` (a fine vintage)
+
 ## Housekeeping
 
 Unless otherwise stated by a suitable header, the files within this repository are made available under the MIT license. If you use this pipeline, an acknowledgement in your work would be nice... Don't forget to [cite Snakemake](https://snakemake.readthedocs.io/en/stable/project_info/citations.html).

Snakefile-base

@@ -424,6 +424,7 @@ rule polish_racon:
 
 rule prepolish_medaka_override_calls2draft:
     singularity: config["medaka_env"],
+    conda: "environments/medaka.yaml" if not config["cuda"] else None
     input:
         contigs=input_polish,
         reads=polish_reads_input,
@@ -462,6 +463,7 @@ rule prepolish_medaka_override_calls2draft_subsample_depth0:
 
 rule polish_medaka:
     singularity: config["medaka_env"],
+    conda: "environments/medaka.yaml" if not config["cuda"] else None
     input:
         contigs=input_polish,
         reads=polish_reads_input,

environments/base-cpu.yaml

@@ -4,24 +4,19 @@ channels:
 dependencies:
   - snakemake-minimal =5.8.1
   - python =3.6
-  - networkx =2.1
-  - matplotlib =2.2.3
-  - bcftools =1.9
-  - samtools =1.9
-  - pysam =0.15.0
-  - pyvcf
-  - pandas
-  - biopython
-  - minimap2
-  - racon
-  - seqtk
-  - kraken2
-  - seqkit
-  - datamash
-  - medaka
+  - pandas =1.1.5
+  - bcftools =1.13
+  - samtools =1.13
+  - pysam =0.17.0
+  - pyvcf =0.6.8
+  - minimap2 =2.22
+  - racon =1.4.20
+  - seqkit =2.0.0
+  - kraken2 =2.1.2
+  - pip
   - pip:
     - git+https://github.com/SamStudio8/bondage.git
     - git+https://github.com/SamStudio8/dehumanizer.git
     - git+https://github.com/SamStudio8/ktkit.git
     - slackclient==1.3.1
-    - GPUtil
+    - GPUtil==1.4.0

environments/medaka.yaml

@@ -0,0 +1,6 @@
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - medaka =0.11.5
+