add codacy yaml and fix some formatting

.codacy.yaml

@@ -0,0 +1,2 @@
+exclude_paths:
+  - "test/**"

sequana_pipelines/lora/config.yaml

@@ -521,7 +521,7 @@ fastp:
 ##       If you want your own multiqc, fill this entry
 multiqc:
     options: -p -f
-    modules: busco quast sequana_coverage prokka fastp long_read_sum
+    modules: busco quast sequana_coverage prokka fastp
     input_directory: .
     config_file: multiqc_config.yaml
     resources:

sequana_pipelines/lora/src/templates/lora.js

@@ -2,32 +2,32 @@
 [].slice.call(document.querySelectorAll("#lora_summary tr"), 1).forEach(row => {
     const selectedClass = "is-selected";
     row.addEventListener("click", () => {
-        /* get row informations */
-        const ths = document.querySelectorAll("#lora_summary th", 1);
+      /* get row informations */
+      const ths = document.querySelectorAll("#lora_summary th", 1);
         const rowObj = [].reduce.call(ths, (acc, th, i) => {
-            const { textContent } = row.cells[i];
-            acc[th.textContent] = textContent;
-            return acc;
+          const { textContent } = row.cells[i];
+          acc[th.textContent] = textContent;
+          return acc;
         }, {});
 
-        /* update row style */
-        if (!row.classList.contains(selectedClass)) {
+      /* update row style */
+      if (!row.classList.contains(selectedClass)) {
             var pastRow = document.getElementById('lora_summary').getElementsByClassName(selectedClass)[0];
-            if (pastRow) {
-                /* hide past row */
-                pastRow.classList.remove(selectedClass);
+        if (pastRow) {
+          /* hide past row */
+          pastRow.classList.remove(selectedClass);
                 const pastRowObj = [].reduce.call(ths, (acc, th, i) => {
-                    const { textContent } = pastRow.cells[i];
+              const { textContent } = pastRow.cells[i];
                     acc[th.textContent] = textContent;
                     return acc;
                 }, {});
                 document.getElementById(pastRowObj.Sample).style.display = "none";
-            }
-            row.classList.add(selectedClass);
-            document.getElementById(rowObj.Sample).style.display = "block";
+        }
+        row.classList.add(selectedClass);
+        document.getElementById(rowObj.Sample).style.display = "block";
         }
     });
-});
+  });
 
 /** open the first contig information*/
 document.getElementById("defaultOpenAssembly").click();

sequana_pipelines/lora/src/templates/summary.js

@@ -1,13 +1,13 @@
 document.body.style.setProperty("--calc-svg-height", "auto");
-const svg = document.getElementsByTagName('svg')[0];
+const svg = document.getElementsByTagName("svg")[0];
 document.body.style.setProperty("--calc-svg-height", svg.getBBox().height + "pt");
 
 document.body.style.setProperty("--calc-dep-height", "auto");
 const tableHeight = document.getElementById('dependencies').firstElementChild.clientHeight + "px";
 document.body.style.setProperty("--calc-dep-height", tableHeight);
 
 document.body.style.setProperty("--calc-methods-height", "auto");
-const methodsHeight = document.getElementById('methods').scrollHeight + "px";
+const methodsHeight = document.getElementById("methods").scrollHeight + "px";
 document.body.style.setProperty("--calc-methods-height", methodsHeight);
 
 /* Hide div */
@@ -19,6 +19,6 @@ const hideDiv = (currentElm, idToHide) => {
   } else {
     elementToHide.classList.remove(`open-section-${idToHide}`);
   }
-  var spanElem = currentElm.querySelector('span');
+  var spanElem = currentElm.querySelector("span");
   spanElem.textContent = spanElem.textContent === "expand_more" ? "expand_less" : "expand_more";
 };