diff --git a/.codacy.yaml b/.codacy.yaml new file mode 100644 index 0000000..c903265 --- /dev/null +++ b/.codacy.yaml @@ -0,0 +1,2 @@ +exclude_paths: + - "test/**" diff --git a/sequana_pipelines/lora/config.yaml b/sequana_pipelines/lora/config.yaml index 4ae911e..c750e72 100644 --- a/sequana_pipelines/lora/config.yaml +++ b/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: diff --git a/sequana_pipelines/lora/src/templates/lora.js b/sequana_pipelines/lora/src/templates/lora.js index 4412869..e107890 100644 --- a/sequana_pipelines/lora/src/templates/lora.js +++ b/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(); diff --git a/sequana_pipelines/lora/src/templates/summary.js b/sequana_pipelines/lora/src/templates/summary.js index 6c7572e..0e3ce11 100644 --- a/sequana_pipelines/lora/src/templates/summary.js +++ b/sequana_pipelines/lora/src/templates/summary.js @@ -1,5 +1,5 @@ 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"); @@ -7,7 +7,7 @@ const tableHeight = document.getElementById('dependencies').firstElementChild.cl 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"; };