Add option to turn off bowtie analyses

.test/config/config.bowtie.yaml

@@ -0,0 +1,33 @@
+samplesheet: resources/samples.tsv
+samples:
+  include:
+    - foo
+    - bar
+  exclude:
+    - foobar
+
+analyses:
+  mapdamage: true
+  authentication: true
+  malt: true
+  bowtie: false
+
+adapters:
+  illumina: true
+  nextera: false
+  custom: []
+
+
+# Databases
+krakenuniq_db: resources/KrakenUniq_DB
+bowtie2_db: resources/ref.fa
+pathogenomesFound: resources/pathogenomesFound.tab
+bowtie2_seqid2taxid_db: resources/seqid2taxid.pathogen.map
+malt_seqid2taxid_db: resources/KrakenUniq_DB/seqid2taxid.map
+malt_nt_fasta: resources/ref.fa
+malt_accession2taxid: resources/accession2taxid.map
+ncbi_db: resources/ncbi
+
+# Breadth and depth of coverage filters
+n_unique_kmers: 1000
+n_tax_reads: 200

.test/runtest.sh

@@ -58,6 +58,17 @@ if [[ -z "$CI" ]]; then
     fi
 fi
 
+
+echo Running workflow excluding bowtie...
+echo snakemake --conda-frontend $CONDA_FRONTEND --use-conda --show-failed-logs --conda-cleanup-pkgs cache -s ../workflow/Snakefile $@
+snakemake --conda-frontend $CONDA_FRONTEND --use-conda --show-failed-logs --conda-cleanup-pkgs cache -s ../workflow/Snakefile --configfile config/config.bowtie.yaml $@
+
+if [ $? -ne 0 ]; then
+    echo ERROR: Workflow test failed!
+    exit
+fi
+
+
 echo Running workflow...
 echo snakemake --conda-frontend $CONDA_FRONTEND --use-conda --show-failed-logs --conda-cleanup-pkgs cache -s ../workflow/Snakefile $@
 snakemake --conda-frontend $CONDA_FRONTEND --use-conda --show-failed-logs --conda-cleanup-pkgs cache -s ../workflow/Snakefile $@

workflow/rules/common.smk

@@ -127,6 +127,8 @@ def all_input(wildcards):
 def mapdamage_input(wildcards):
     if not config["analyses"]["mapdamage"]:
         return []
+    if not config["analyses"]["bowtie"]:
+        return []
     return expand("results/MAPDAMAGE/{sample}", sample=SAMPLES)
 
 
@@ -166,8 +168,9 @@ def multiqc_input(wildcards):
         "cutadapt": expand(
             "logs/CUTADAPT_ADAPTER_TRIMMING/{sample}.log", sample=SAMPLES
         ),
-        "bowtie2": expand("logs/BOWTIE2/{sample}.log", sample=SAMPLES),
     }
+    if config["analyses"]["bowtie"]:
+        d["bowtie2"] = expand("logs/BOWTIE2/{sample}.log", sample=SAMPLES)
     return d
 
 

workflow/schemas/config.schema.yaml

@@ -17,24 +17,29 @@ definitions:
     type: object
     default: {}
     properties:
-      mapdamage:
+      authentication:
         description: >-
-          mapdamage analysis
+          authentication analysis
         type: boolean
         default: true
-      authentication:
+      bowtie:
         description: >-
-          authentication analysis
+          bowtie analysis
+        type: boolean
+        default: true
+      krona:
+        description: >-
+          krona analysis
         type: boolean
         default: true
       malt:
         description: >-
           malt analysis
         type: boolean
         default: true
-      krona:
+      mapdamage:
         description: >-
-          krona analysis
+          mapdamage analysis
         type: boolean
         default: true