Release v2.1.0

.github/scripts/bump_version.py

@@ -13,6 +13,15 @@
 
 major, minor, patch = map(int, m.groups())
 
+print(
+    "Before",
+    f"label: {label}",
+    f"major: {major}",
+    f"minor: {minor}",
+    f"patch: {patch}",
+    sep = "\n"
+)
+
 if label == "major":
     major += 1
     minor = 0
@@ -32,13 +41,16 @@
 
 new_version = f'{major}.{minor}.{patch}'
 
-text = re.sub(
-    r'__version__ = ".*"',
-    f'__version__ = "{new_version}"',
-    text,
+print(
+    "After",
+    "new_version: {new_version}",
+    f"major: {major}",
+    f"minor: {minor}",
+    f"patch: {patch}",
+    sep = "\n"
 )
 
-version_file.write_text(text)
+version_file.write_text(new_version)
 
 # Write new version to Github actions
 if "GITHUB_OUTPUT" in os.environ:

.github/workflows/comments.yml

@@ -1,4 +1,4 @@
-name: Commands
+name: Update PR Labels
 on:
   issue_comment:
     types: [created]

.github/workflows/version.yml

@@ -44,12 +44,14 @@ jobs:
         run: |
           git config user.name github-actions
           git config user.email github-actions@github.com
-
+      
           git add src/mmaseq/__version__.py
-
-          # Reference the output generated by your python script
-          NEW_VER="${{ steps.bumper.outputs.new_version }}"
 
-          git commit -m "Bump version to v$NEW_VER"
-          git push
-
+          # Only commit if there are staged changes
+          if ! git diff-index --quiet --cached HEAD --; then
+            NEW_VER="${{ steps.bumper.outputs.new_version }}"
+            git commit -m "Bump version to v$NEW_VER"
+            git push
+          else
+            echo "No changes detected, skipping commit"
+          fi

src/mmaseq/__version__.py

@@ -1 +1 @@
-__version__ = "2.0.0"
+2.1.0

src/mmaseq/config/species_configs/A_pleuropneumoniae.yaml

@@ -0,0 +1,2 @@
+serovar_detector:
+    reads: True

src/mmaseq/config/species_configs/test.yaml

@@ -98,3 +98,6 @@ sistr:
 kmeraligner:
     database : [vancomycin, vancomycinOperon]
     reads: True
+
+serovar_detector:
+    reads: True

src/mmaseq/data/samplesheet.tsv

@@ -6,3 +6,4 @@ SRR26205262	reads/SRR26205262_1.fastq.gz	reads/SRR26205262_2.fastq.gz	assemblies
 ERR2929615	reads/ERR2929615_1.fastq.gz	reads/ERR2929615_2.fastq.gz	assemblies/ERR2929615.fasta	E_Faecalis.yaml
 ERR2929578	reads/ERR2929578_1.fastq.gz	reads/ERR2929578_2.fastq.gz	assemblies/ERR2929578.fasta	E_Faecium.yaml
 ERR142064	reads/ERR142064_1.fastq.gz	reads/ERR142064_2.fastq.gz	assemblies/ERR142064.fasta	C_difficile.yaml
+ERR14229029	reads/ERR14229029_1.fastq.gz	reads/ERR14229029_2.fastq.gz	assemblies/ERR14229029.fasta	A_pleuropneumoniae.yaml

src/mmaseq/workflow/envs/serovar_detector.yaml

@@ -0,0 +1,3 @@
+name: serovar_detector
+dependencies:
+  - bioconda::serovar_detector

src/mmaseq/workflow/rules/Analysis.smk

@@ -453,6 +453,32 @@ rule serotypefinder:
         mv $OUTDIR/{params.tmp_results} {output.results} >> {log.stdout} 2>&1
         """
 
+
+rule serovar_detector:
+    input:
+        assembly = rules.assembly.output.assembly
+    params:
+        tmp_results = "serovars.tsv"
+    output:
+        results = f"{outdir}/{{sample}}/raw/serovar_detector/serovar_detector.tsv"
+    conda:
+        ENVS_DIR / "serovar_detector.yaml"
+    log:
+        stdout = f"{logdir}/serovar_detector_{{sample}}.log"
+    shell:
+        """
+        OUTDIR=$(dirname {output.results})
+
+        cmd="serovar_detector -A {input.assembly} -o $OUTDIR -t 1"
+
+        echo "Executing command:\n$cmd\n" > {log.stdout} 2>&1
+        eval $cmd >> {log.stdout} 2>&1
+
+        echo "Renaming result files" >> {log.stdout} 2>&1
+        mv $OUTDIR/{params.tmp_results} {output.results} >> {log.stdout} 2>&1
+        """
+
+
 ### SNP Analysis ###
 
 # Samtools and bcftools

src/mmaseq/workflow/rules/Paired_Reads.smk

@@ -385,6 +385,33 @@ rule PR_serotypefinder:
         mv $OUTDIR/{params.tmp_results} {output.results} >> {log.stdout} 2>&1
         """
 
+
+rule PR_serovar_detector:
+    input:
+        R1 = lambda wc: samplesheet.loc[wc.sample, "read1"],
+        R2 = lambda wc: samplesheet.loc[wc.sample, "read2"]
+    params:
+        tmp_results = "serovars.tsv"
+    output:
+        results = f"{outdir}/{{sample}}/raw/PR/serovar_detector/serovar_detector.tsv"
+    conda:
+        ENVS_DIR / "serovar_detector.yaml"
+    log:
+        stdout = f"{logdir}/PR/serovar_detector_{{sample}}.log"
+    shell:
+        """
+        OUTDIR=$(dirname {output.results})
+
+        cmd="serovar_detector -1 {input.R1} -2 {input.R2} -o $OUTDIR -t 1"
+
+        echo "Executing command:\n$cmd\n" > {log.stdout} 2>&1
+        eval $cmd >> {log.stdout} 2>&1
+
+        echo "Renaming result files" >> {log.stdout} 2>&1
+        mv $OUTDIR/{params.tmp_results} {output.results} >> {log.stdout} 2>&1
+        """
+
+
 rule PR_lrefinder:
     input:
         res = rules.PR_kmeraligner.output.results,