Merge pull request #1823 from nf-core/muffato-patch-1

Explain we don't want MD5 checksums for `versions.yml`

markdown/developers/modules.md

@@ -126,6 +126,8 @@ We have implemented a number of commands in the `nf-core/tools` package to make
 
       `md5sum` checks are the preferable choice of test to determine file changes, however, this may not be possible for all outputs generated by some tools e.g. if they include time stamps or command-related headers. Please do your best to avoid just checking for the file being present e.g. it may still be possible to check that the file contains the appropriate text snippets.
 
+      > Leave the `versions.yml` entry _without_ a MD5 checksum. Its content will change every time we bump the version of the software.
+
 8. Create a yaml file containing information required for module unit testing
 
    ```console

public_html/assets/js/aws-s3-explorer.js

@@ -232,7 +232,7 @@ $(function () {
     if (data.params.Prefix) {
       parts.push.apply(
         parts,
-        data.params.Prefix.endsWith('/') ? data.params.Prefix.slice(0, -1).split('/') : data.params.Prefix.split('/')
+        data.params.Prefix.endsWith('/') ? data.params.Prefix.slice(0, -1).split('/') : data.params.Prefix.split('/'),
       );
     }
 

public_html/assets/js/canvas2svg.js

@@ -111,7 +111,7 @@
       'Scaron,b1,scaron,bo,Yuml,m6,circ,ms,tilde,802,ensp,803,emsp,809,thinsp,80c,zwnj,80d,zwj,80e,lrm,' +
       '80f,rlm,80j,ndash,80k,mdash,80o,lsquo,80p,rsquo,80q,sbquo,80s,ldquo,80t,rdquo,80u,bdquo,810,dagger,' +
       '811,Dagger,81g,permil,81p,lsaquo,81q,rsaquo,85c,euro',
-    32
+    32,
   );
 
   //Some basic mappings for attributes and default values.
@@ -415,7 +415,7 @@
             matches = regex.exec(value);
             currentElement.setAttribute(
               style.svgAttr,
-              format('rgb({r},{g},{b})', { r: matches[1], g: matches[2], b: matches[3] })
+              format('rgb({r},{g},{b})', { r: matches[1], g: matches[2], b: matches[3] }),
             );
             //should take globalAlpha here
             var opacity = matches[4];
@@ -671,7 +671,7 @@
         cp2y: cp2y,
         x: x,
         y: y,
-      })
+      }),
     );
   };
 
@@ -823,7 +823,7 @@
         width: width,
         height: height,
       },
-      true
+      true,
     );
     parent = this.__closestGroupOrSvg();
     parent.appendChild(rect);
@@ -848,7 +848,7 @@
         width: width,
         height: height,
       },
-      true
+      true,
     );
     parent = this.__closestGroupOrSvg();
     parent.appendChild(rect);
@@ -899,7 +899,7 @@
         height: height,
         fill: '#FFFFFF',
       },
-      true
+      true,
     );
     parent.appendChild(rect);
   };
@@ -919,7 +919,7 @@
         y2: y2 + 'px',
         gradientUnits: 'userSpaceOnUse',
       },
-      false
+      false,
     );
     this.__defs.appendChild(grad);
     return new CanvasGradient(grad, this);
@@ -941,7 +941,7 @@
         fy: y0 + 'px',
         gradientUnits: 'userSpaceOnUse',
       },
-      false
+      false,
     );
     this.__defs.appendChild(grad);
     return new CanvasGradient(grad, this);
@@ -1018,7 +1018,7 @@
           'text-anchor': getTextAnchor(this.textAlign),
           'dominant-baseline': getDominantBaseline(this.textBaseline),
         },
-        true
+        true,
       );
 
     textElement.appendChild(this.__document.createTextNode(text));
@@ -1100,7 +1100,7 @@
         sweepFlag: sweepFlag,
         endX: endX,
         endY: endY,
-      })
+      }),
     );
 
     this.__currentPosition = { x: endX, y: endY };
@@ -1234,7 +1234,7 @@
       svgImage.setAttributeNS(
         'http://www.w3.org/1999/xlink',
         'xlink:href',
-        image.nodeName === 'CANVAS' ? image.toDataURL() : image.getAttribute('src')
+        image.nodeName === 'CANVAS' ? image.toDataURL() : image.getAttribute('src'),
       );
       parent.appendChild(svgImage);
     }
@@ -1257,7 +1257,7 @@
       img.setAttributeNS(
         'http://www.w3.org/1999/xlink',
         'xlink:href',
-        image.nodeName === 'CANVAS' ? image.toDataURL() : image.getAttribute('src')
+        image.nodeName === 'CANVAS' ? image.toDataURL() : image.getAttribute('src'),
       );
       pattern.appendChild(img);
       this.__defs.appendChild(pattern);

public_html/assets/js/nf-core-schema-builder.js

@@ -21,7 +21,7 @@ $(function () {
       .calendar()
       .replace(/^\w/, function (chr) {
         return chr.toLowerCase();
-      })
+      }),
   );
   $('.cache_expires_at').show();
 
@@ -105,7 +105,7 @@ $(function () {
               search_term +
               "'], .popover-body div button[data-classname*='" +
               search_term +
-              "']"
+              "']",
           )
           .show();
       }
@@ -294,14 +294,14 @@ $(function () {
     } else {
       $('.add-param-btn, .add-group-btn, .collapse-groups-btn, .expand-groups-btn, .to-top-btn').attr(
         'disabled',
-        false
+        false,
       );
     }
 
     // Warn about the console finishing
     if ($(this).hasClass('back-to-editor-btn')) {
       alert(
-        'nf-core schema build will have now exited. Any further change will have to be manually copied to your schema file. Note that you can run nf-core schema build as often as you like for updates.'
+        'nf-core schema build will have now exited. Any further change will have to be manually copied to your schema file. Note that you can run nf-core schema build as often as you like for updates.',
       );
     }
   });
@@ -776,7 +776,7 @@ $(function () {
       var help_text_html = md_converter.makeHtml($('#help_text_input').val());
       $('.helptext-html-preview .helptext-preview-helptext').html(help_text_html);
       $('.helptext-html-preview .helptext-preview-helptext table').addClass(
-        'table table-bordered table-striped table-sm small'
+        'table table-bordered table-striped table-sm small',
       );
       $('.helptext-html-preview .helptext-preview-helptext table').wrap('<div class="table-responsive"></div>');
     }
@@ -937,7 +937,7 @@ $(function () {
         var number_val = parseFloat(el);
         if (isNaN(number_val)) {
           $('.modal-body').append(
-            '<div class="alert alert-danger">Error: Enumerated values have to be numeric for parameter types "integer" and "number".</div>'
+            '<div class="alert alert-danger">Error: Enumerated values have to be numeric for parameter types "integer" and "number".</div>',
           );
           e.preventDefault();
           e.stopPropagation();
@@ -1324,10 +1324,10 @@ function generate_param_row(id, param) {
     var re = new RegExp('^fa[a-z -]+$');
     if (!re.test(param['fa_icon'])) {
       console.error(
-        "FontAwesome icon did not match the regex: /^fa[a-z -]+$/ ('" + param['fa_icon'] + "') - removing from schema."
+        "FontAwesome icon did not match the regex: /^fa[a-z -]+$/ ('" + param['fa_icon'] + "') - removing from schema.",
       );
       alert(
-        "FontAwesome icon did not match the regex: /^fa[a-z -]+$/ ('" + param['fa_icon'] + "') - removing from schema."
+        "FontAwesome icon did not match the regex: /^fa[a-z -]+$/ ('" + param['fa_icon'] + "') - removing from schema.",
       );
       delete param['fa_icon'];
       update_param_in_schema(id, param);
@@ -1438,7 +1438,7 @@ function generate_group_row(id, param, child_params) {
     var re = new RegExp('^fa[a-z -]+$');
     if (!re.test(param['fa_icon'])) {
       console.error(
-        "FontAwesome icon did not match the regex: /^fa[a-z -]+$/ ('" + param['fa_icon'] + "') - removing from schema."
+        "FontAwesome icon did not match the regex: /^fa[a-z -]+$/ ('" + param['fa_icon'] + "') - removing from schema.",
       );
       delete param['fa_icon'];
       update_param_in_schema(id, param);
@@ -1622,7 +1622,7 @@ function validate_param(param) {
           'Error: Default value "' +
             param['default'] +
             '" must be greater than or equal to minimum value: ' +
-            param['minimum']
+            param['minimum'],
         );
         return false;
       }
@@ -1633,7 +1633,7 @@ function validate_param(param) {
           'Error: Default value "' +
             param['default'] +
             '" must be less than or equal to maximum value: ' +
-            param['maximum']
+            param['maximum'],
         );
         return false;
       }
@@ -1670,7 +1670,7 @@ function validate_param(param) {
         'Error: Default value "' +
           param['default'] +
           '" must be one of the Enumerated values: ' +
-          param['enum'].join(', ')
+          param['enum'].join(', '),
       );
       return false;
     }
@@ -1681,7 +1681,7 @@ function validate_param(param) {
     var re = new RegExp(param['pattern']);
     if (!re.test(param['default'])) {
       alert(
-        'Error: Default value "' + param['default'] + '" must match the parameter pattern regex: ' + param['pattern']
+        'Error: Default value "' + param['default'] + '" must match the parameter pattern regex: ' + param['pattern'],
       );
       return false;
     }

public_html/assets/js/nf-core-schema-launcher.js

@@ -15,7 +15,7 @@ $(function () {
       .calendar()
       .replace(/^\w/, function (chr) {
         return chr.toLowerCase();
-      })
+      }),
   );
   $('.cache_expires_at').show();
 
@@ -120,7 +120,7 @@ function set_validation_styles(form_is_valid) {
   // Reset
   $('#validation_fail_list').html('');
   $('.form-control:has(.form-check-input[type="radio"])').removeClass(
-    'radio-form-control-valid radio-form-control-invalid'
+    'radio-form-control-valid radio-form-control-invalid',
   );
   $('.input-group .input-group-prepend').removeClass('input-group-valid input-group-invalid');
 
@@ -141,7 +141,7 @@ function set_validation_styles(form_is_valid) {
           $(this).attr('id') +
           '" class="scroll_to_link"><code>' +
           $(this).attr('name').replace('params_', '--').replace('nxf_flag_', '') +
-          '</code></a></li>'
+          '</code></a></li>',
       );
     });
   }

public_html/assets/js/nf-core.js

@@ -36,7 +36,7 @@ $(function () {
     let $this = $(this);
     $this.addClass('position-relative');
     var $copy_btn = $(
-      '<button class="btn btn-outline-secondary copy-button position-absolute top-0 end-0" data-bs-toggle="tooltip"  data-bs-placement="left" data-bs-original-title="Copy to clipboard" ><i class="fas fa-clipboard fa-swap-opacity"></i></button>'
+      '<button class="btn btn-outline-secondary copy-button position-absolute top-0 end-0" data-bs-toggle="tooltip"  data-bs-placement="left" data-bs-original-title="Copy to clipboard" ><i class="fas fa-clipboard fa-swap-opacity"></i></button>',
     );
     $this.append($copy_btn);
     var btn_tooltip = new bootstrap.Tooltip($copy_btn, { container: 'body' });
@@ -493,6 +493,6 @@ function scroll_to(target_el, offset) {
     {
       scrollTop: el_offset,
     },
-    500
+    500,
   );
 }

public_html/assets/js/transcripts.js

@@ -84,7 +84,7 @@ function highlight(event) {
                 $('details[open]').scrollTop() -
                 1.2 * parseFloat(getComputedStyle(document.documentElement).fontSize), // convert rem into px
             },
-            'slow'
+            'slow',
           );
         }
       }

public_html/assets/scss/_nf-core.scss

@@ -568,8 +568,12 @@ h4:focus .header-link,
 
 .edit-md-btn {
   opacity: 0.5;
-  transition: opacity 0.15s ease-in-out, color 0.15s ease-in-out, background-color 0.15s ease-in-out,
-    border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out;
+  transition:
+    opacity 0.15s ease-in-out,
+    color 0.15s ease-in-out,
+    background-color 0.15s ease-in-out,
+    border-color 0.15s ease-in-out,
+    box-shadow 0.15s ease-in-out;
 }
 .edit-md-btn:hover,
 .edit-md-btn:active,