update unicycler to add long read option

.github/workflows/main.yml

@@ -14,6 +14,13 @@ on:
 jobs:
   testing:
     runs-on: ubuntu-latest
+    strategy:
+       max-parallel: 5
+       matrix:
+         python: ['3.10']
+
+
+
     steps:
     - name: checkout git repo
       uses: actions/checkout@v4
@@ -26,10 +33,13 @@ jobs:
     - name: mamba
       uses: "mamba-org/setup-micromamba@v1"
       with:
+          # snakemake complains it cannot find mamba. the micromamba does not seem 
+          # to install mamba by itself so we add it specifically
           create-args: >-
               python=${{ matrix.python }}
               snakemake-minimal
               pytest
+              mamba
           environment-name: snakemake
           init-shell: >-
             bash
@@ -45,7 +55,7 @@ jobs:
       run: |
         git fetch origin main
     - name: Test with pytest
-      shell: bash -el {0}
+      shell: micromamba-shell {0}
       env:
         DIFF_MASTER: ${{ github.event_name == 'pull_request' }}
         DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }}
@@ -55,5 +65,4 @@ jobs:
         else
           echo "No parent commit. Skipping git diff."
         fi
-        #/home/runner/micromamba-bin/micromamba activate snakemake
         pytest test.py -vv

wrappers/unicycler/README.md

@@ -4,7 +4,7 @@ This wrapper generates de novo assembly using **Unicycler** an assembly pipeline
 
 **Required input:**
 
-- **fastq**: the input fastq files.
+- **fastq**: the input fastq files. Could be short (paired or not) or long reads
 
 **Required output::**
 
@@ -15,6 +15,11 @@ This wrapper generates de novo assembly using **Unicycler** an assembly pipeline
 - **mode**: Bridging mode. (conservative|normal|bold) (default: "normal")
 - **options**: a list of valid **Unicycler** options.
 
+**Optional parameters:**
+
+- **long_reads** if provided and set to True, unicycler is used for long reads.
+  expected input is therefore single end data (one file).
+
 Notes: This wrapper cannot be used to perform correction only.
 
 **Log:**
@@ -33,9 +38,11 @@ Notes: This wrapper cannot be used to perform correction only.
     # - mode: any bridging mode in this list ["conservative", "normal", "bold"]
     # - options: any options recognised by unicycler cli.
     # - threads: number of threads to be used.
+    # - long_reads: set to True to switch to long read analysis
     #
     unicycler:
         mode: "normal"
+        long_reads: True # optional
         options: ""
         threads: 4
 
@@ -54,6 +61,7 @@ Notes: This wrapper cannot be used to perform correction only.
             "logs/unicycler.log"
         threads:
             config["unicycler"]["threads"]
+        container: 
         wrapper:
             "main/wrappers/unicycler"
 

wrappers/unicycler/test/Snakefile

@@ -10,3 +10,4 @@ rule unicycler:
         "unicycler.log"
     wrapper:
         "main/wrappers/unicycler"
+

wrappers/unicycler/wrapper.py

@@ -19,9 +19,16 @@
 contigs = snakemake.output
 logs = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
+# by default, this wrapper is for short read data
 is_paired = len(fastq) == 2
 input_file = f"-1 {fastq[0]} -2 {fastq[1]}" if is_paired else f"-s {fastq[0]}"
 
+# but the presence of long_reads set to True in the params section
+# allows us to switch to the long read case
+
+if snakemake.params.get("long_reads", False):
+    input_file = f" -l {fastq[0]}"
+
 options = snakemake.params.get("options", "")
 mode = snakemake.params.get("mode", "normal")
 outdir = Path(str(contigs)).parent