nf-core · jfy133 · May 14, 2021 · May 11, 2021 · May 12, 2021 · May 12, 2021
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -10,14 +10,15 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
 -->
+<!-- markdownlint-disable ul-indent -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+    - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](<https://github.com/>nf-core/eager/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -8,6 +8,9 @@ on:
   release:
     types: [published]
 
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
 jobs:
   test:
     name: Run workflow tests
@@ -20,7 +23,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.07.1', '21.03.0-edge']
+        nxf_ver: ['20.07.1', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,18 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - Fixed some missing or incorrectly reported software versions
 
+## v2.3.5dev - [date]
+
+### `Added`
+
+- [#722](https://github.com/nf-core/eager/issues/722) - Adds bwa `-o` flag for more flexibility in bwa parameters
+- [#736](https://github.com/nf-core/eager/issues/736) - Add printing of multiqc run report location on successful completion
+
+### `Fixed`
+
+- [#723](https://github.com/nf-core/eager/issues/723) - Fixes empty fields in TSV resulting in uninformative error
+- Updated template to nf-core/tools 1.14
+
 ### `Dependencies`
 
 ### `Deprecated`

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nfcore/base:1.13.3
+FROM nfcore/base:1.14
 LABEL authors="The nf-core/eager community" \
       description="Docker image containing all software requirements for the nf-core/eager pipeline"
 
@@ -11,7 +11,3 @@ ENV PATH /opt/conda/envs/nf-core-eager-2.3.5dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
 RUN conda env export --name nf-core-eager-2.3.5dev > nf-core-eager-2.3.5dev.yml
-
-# Instruct R processes to use these empty files instead of clashing with a local version
-RUN touch .Rprofile
-RUN touch .Renviron
diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Quick Start
 
-1. Install [`nextflow`](https://nf-co.re/usage/installation) (version >= 20.04.0)
+1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.07.1`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 

diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
@@ -112,8 +112,14 @@ class NfcoreSchema {
             }
             // unexpected params
             def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
-            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam)) {
-                unexpectedParams.push(specifiedParam)
+            def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
+            def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
+            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !expectedParamsLowerCase.contains(specifiedParamLowerCase)) {
+                // Temporarily remove camelCase/camel-case params #1035
+                def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
+                if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
+                    unexpectedParams.push(specifiedParam)
+                }
             }
         }
 
@@ -191,11 +197,11 @@ class NfcoreSchema {
 
     // Remove an element from a JSONArray
     private static JSONArray removeElement(jsonArray, element){
-        def list = []  
+        def list = []
         int len = jsonArray.length()
-        for (int i=0;i<len;i++){ 
+        for (int i=0;i<len;i++){
             list.add(jsonArray.get(i).toString())
-        } 
+        }
         list.remove(element)
         JSONArray jsArray = new JSONArray(list)
         return jsArray
@@ -213,7 +219,7 @@ class NfcoreSchema {
                             // If the param was required, change this
                             if (definition[key].has("required")) {
                                 def cleaned_required = removeElement(definition[key].required, ignore_param)
-                                definition[key].put("required", cleaned_required) 
+                                definition[key].put("required", cleaned_required)
                             }
                         }
                     }
@@ -243,7 +249,7 @@ class NfcoreSchema {
             }
             // Cast Duration to String
             if (p['value'].getClass() == nextflow.util.Duration) {
-                new_params.replace(p.key, p['value'].toString())
+                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
             }
             // Cast LinkedHashMap to String
             if (p['value'].getClass() == LinkedHashMap) {
@@ -482,10 +488,10 @@ class NfcoreSchema {
         }
         workflow_summary['runName']      = workflow.runName
         if (workflow.containerEngine) {
-            workflow_summary['containerEngine'] = "$workflow.containerEngine"
+            workflow_summary['containerEngine'] = workflow.containerEngine
         }
         if (workflow.container) {
-            workflow_summary['container']       = "$workflow.container"
+            workflow_summary['container'] = workflow.container
         }
         workflow_summary['launchDir']    = workflow.launchDir
         workflow_summary['workDir']      = workflow.workDir
@@ -506,17 +512,7 @@ class NfcoreSchema {
                     def params_value = params.get(param)
                     def schema_value = group_params.get(param).default
                     def param_type   = group_params.get(param).type
-                    if (schema_value == null) {
-                        if (param_type == 'boolean') {
-                            schema_value = false
-                        }
-                        if (param_type == 'string') {
-                            schema_value = ''
-                        }
-                        if (param_type == 'integer') {
-                            schema_value = 0
-                        }
-                    } else {
+                    if (schema_value != null) {
                         if (param_type == 'string') {
                             if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
                                 def sub_string = schema_value.replace('\$projectDir', '')
@@ -535,8 +531,13 @@ class NfcoreSchema {
                         }
                     }
 
-                    if (params_value != schema_value) {
-                        sub_params.put("$param", params_value)
+                    // We have a default in the schema, and this isn't it
+                    if (schema_value != null && params_value != schema_value) {
+                        sub_params.put(param, params_value)
+                    }
+                    // No default in the schema, and this isn't empty
+                    else if (schema_value == null && params_value != "" && params_value != null && params_value != false) {
+                        sub_params.put(param, params_value)
                     }
                 }
             }
@@ -549,22 +550,23 @@ class NfcoreSchema {
      * Beautify parameters for summary and return as string
      */
     private static String params_summary_log(workflow, params, json_schema) {
+        Map colors = log_colours(params.monochrome_logs)
         String output  = ''
         def params_map = params_summary_map(workflow, params, json_schema)
         def max_chars  = params_max_chars(params_map)
         for (group in params_map.keySet()) {
             def group_params = params_map.get(group)  // This gets the parameters of that particular group
             if (group_params) {
-                output += group + '\n'
+                output += colors.bold + group + colors.reset + '\n'
                 for (param in group_params.keySet()) {
-                    output += "    \u001B[1m" +  param.padRight(max_chars) + ": \u001B[1m" + group_params.get(param) + '\n'
+                    output += "  " + colors.blue + param.padRight(max_chars) + ": " + colors.green +  group_params.get(param) + colors.reset + '\n'
                 }
                 output += '\n'
             }
         }
-        output += "[Only displaying parameters that differ from pipeline default]\n"
         output += dashed_line(params.monochrome_logs)
-        output += '\n\n' + dashed_line(params.monochrome_logs)
+        output += colors.dim + "\n Only displaying parameters that differ from defaults.\n" + colors.reset
+        output += dashed_line(params.monochrome_logs)
         return output
     }