Updated all dependencies, wrappers and actions; adapted to use mamba

Author: AntonieV

.github/workflows/main.yaml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Lint workflow
-        uses: snakemake/snakemake-github-action@v1.23.0
+        uses: snakemake/snakemake-github-action@v1.24.0
         with:
           directory: .test
           snakefile: workflow/Snakefile
@@ -28,14 +28,14 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Test workflow
-      uses: snakemake/snakemake-github-action@v1.23.0
+      uses: snakemake/snakemake-github-action@v1.24.0
       with:
         directory: .test
         snakefile: workflow/Snakefile
-        args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --conda-frontend mamba"
+        args: "--use-conda  --conda-frontend mamba --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --conda-frontend mamba"
 
     - name: Test report
-      uses: snakemake/snakemake-github-action@v1.23.0
+      uses: snakemake/snakemake-github-action@v1.24.0
       with:
         directory: .test
         snakefile: workflow/Snakefile

README.md

@@ -63,7 +63,7 @@ If you use this workflow in a paper, don't forget to give credits to the authors
 
 ### Step 1: Obtain a copy of this workflow
 
-1. Create a new github repository using this workflow [as a template](https://help.github.com/en/articles/creating-a-repository-from-a-template).
+1. Create a new GitHub repository using this workflow [as a template](https://help.github.com/en/articles/creating-a-repository-from-a-template).
 2. [Clone](https://help.github.com/en/articles/cloning-a-repository) the newly created repository to your local system, into the place where you want to perform the data analysis.
 
 ### Step 2: Configure workflow
@@ -72,9 +72,12 @@ Configure the workflow according to your needs via editing the files in the `con
 
 ### Step 3: Install Snakemake
 
-Install Snakemake using [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html):
-
+1. Install [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
+2. Install [mamba](https://github.com/mamba-org/mamba) in conda base and create a snakemake conda environment:
+```bash
+    conda install -n base -c conda-forge mamba
     conda create -c bioconda -c conda-forge -n snakemake snakemake
+```
 
 For installation details, see the [instructions in the Snakemake documentation](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html).
 
@@ -88,23 +91,23 @@ Activate the conda environment:
 
 Test your configuration by performing a dry-run via
 
-    snakemake --use-conda -n
+    snakemake --use-conda --conda-frontend mamba -n
 
 Execute the workflow locally via
 
-    snakemake --use-conda --cores $N
+    snakemake --use-conda --conda-frontend mamba --cores $N
 
 using `$N` cores or run it in a cluster environment via
 
-    snakemake --use-conda --cluster qsub --jobs 100
+    snakemake --use-conda --conda-frontend mamba --cluster qsub --jobs 100
 
 or
 
-    snakemake --use-conda --drmaa --jobs 100
+    snakemake --use-conda --conda-frontend mamba --drmaa --jobs 100
 
 If you not only want to fix the software stack but also the underlying OS, use
 
-    snakemake --use-conda --use-singularity
+    snakemake --use-conda --conda-frontend mamba --use-singularity
 
 in combination with any of the modes above.
 See the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executable.html) for further details.

start.sh

@@ -43,7 +43,7 @@ source ~/miniconda3/etc/profile.d/conda.sh
 
 conda activate snakemake
 
-snakemake --use-conda --cores $(nproc) --show-failed-logs --conda-cleanup-pkgs cache -R all
+snakemake --use-conda --conda-frontend mamba --cores $(nproc) --show-failed-logs --conda-cleanup-pkgs cache -R all
 
 snakemake --report
 

start_test.sh

@@ -43,7 +43,7 @@ source ~/miniconda3/etc/profile.d/conda.sh
 
 conda activate snakemake
 
-snakemake --use-conda --cores $(nproc) --directory .test --show-failed-logs --conda-cleanup-pkgs cache -R all
+snakemake --use-conda --conda-frontend mamba --cores $(nproc) --directory .test --show-failed-logs --conda-cleanup-pkgs cache -R all
 
 snakemake --report --directory .test
 

workflow/envs/blast.yaml

@@ -2,5 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - blast ==2.10.1
-  - openssl >=1.0
+  - blast ==2.13.0
+  - openssl ==3.1.0

workflow/envs/cutadapt_se.yaml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - cutadapt ==2.10
+  - cutadapt ==4.3

workflow/envs/noderad.yaml

@@ -7,9 +7,9 @@ dependencies:
   - xorg-libxi ==1.7.10
   - xorg-libxcursor ==1.2.0
   - xorg-libxdamage ==1.1.5
-  - xorg-libxcomposite ==0.4.5
+  - xorg-libxcomposite ==0.4.6
   - xorg-libxrandr ==1.5.2
-  - xorg-libxinerama ==1.1.4
-  - graph-tool ==2.37
-  - pysam ==0.16
-  - biopython ==1.78
+  - xorg-libxinerama ==1.1.5
+  - graph-tool ==2.53
+  - pysam ==0.21.0
+  - biopython ==1.81

workflow/envs/plots_blast.yaml

@@ -2,5 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - r-tidyverse ==1.3.0
-  - r-stringr ==1.4.0
+  - r-tidyverse ==2.0.0
+  - r-stringr ==1.5.0

workflow/envs/sim_to_fasta.yaml

@@ -2,4 +2,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - pyyaml ==5.3
+  - pyyaml ==6.0

workflow/rules/evaluation.smk

@@ -38,7 +38,7 @@ rule samtools_index:
     log:
         "logs/evaluation/index/{type}_fasta/{sample}.{type}.fasta"
     wrapper:
-        "v0.69.0/bio/samtools/faidx"
+        "v1.25.0/bio/samtools/faidx"
 
 rule blast_database:
     input:

workflow/rules/noderad.smk

@@ -7,7 +7,7 @@ rule minimap2_index:
         "logs/minimap2/{sample}.log"
     threads: 3
     wrapper:
-        "0.66.0/bio/minimap2/index"
+        "v1.25.0/bio/minimap2/index"
 
 # determine edit distances and best alignment with minimap2
 rule minimap2:
@@ -22,7 +22,7 @@ rule minimap2:
         extra="-a -A 10 -N 100 --eqx --cs=long"
     threads: 3
     wrapper:
-        "0.66.0/bio/minimap2/aligner"
+        "v1.25.0/bio/minimap2/aligner"
 
 # converts SAM files to BAM files
 rule samtools_view:
@@ -35,7 +35,7 @@ rule samtools_view:
     params:
         " -b "
     wrapper:
-        "v0.69.0/bio/samtools/view"
+        "v1.25.0/bio/samtools/view"
 
 # RADSeq analysis: calulates alleles and loci likelihoods and returns vcf file with with the most probable loci
 rule noderad:

workflow/rules/qc.smk

@@ -9,7 +9,7 @@ rule fastqc:
     log:
         "logs/qc/fastqc/{sample}_fastqc.log"
     wrapper:
-        "0.66.0/bio/fastqc"
+        "v1.25.0/bio/fastqc"
 
 rule multiqc:
     input:
@@ -19,4 +19,4 @@ rule multiqc:
     log:
         "logs/qc/multiqc.log"
     wrapper:
-        "0.66.0/bio/multiqc"
+        "v1.25.0/bio/multiqc"