Add and fix ECLint in pipeline

.editorconfig

@@ -0,0 +1,24 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
+
+# These files are edited upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,8 +16,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
 
 - [ ] 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 - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
- - [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/rnaseq _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.

.github/workflows/linting.yml

@@ -8,18 +8,17 @@ on:
     types: [published]
 
 jobs:
-
   Markdown:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-node@v1
         with:
-          node-version: '10'
+          node-version: "10"
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
-        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.markdownlint.yml
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -47,14 +46,28 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-node@v1
+        with:
+          node-version: "10"
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
 
   YAML:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
       - uses: actions/setup-node@v1
         with:
-          node-version: '10'
+          node-version: "10"
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
@@ -88,7 +101,6 @@ jobs:
   nf-core:
     runs-on: ubuntu-latest
     steps:
-
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
@@ -101,8 +113,8 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: '3.6'
-          architecture: 'x64'
+          python-version: "3.6"
+          architecture: "x64"
 
       - name: Install dependencies
         run: |
@@ -129,4 +141,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-

.github/markdownlint.yml → .markdownlint.yml

@@ -1,6 +1,8 @@
 # Markdownlint configuration file
 default: true
 line-length: false
+ul-indent:
+    indent: 4
 no-duplicate-header:
     siblings_only: true
 no-inline-html:
@@ -10,3 +12,5 @@ no-inline-html:
         - kbd
         - details
         - summary
+single-title:
+    level: 2

.nf-core-lint.yaml

@@ -4,7 +4,10 @@ files_unchanged:
   - assets/email_template.html
   - assets/email_template.txt
   - assets/multiqc_config.yaml
+  - assets/sendmail_template.txt
   - lib/NfcoreSchema.groovy
+  - docs/README.md
 files_exist:
+  - .github/markdownlint.yml
   - bin/markdown_to_html.py
 actions_awsfulltest: False

CHANGELOG.md

@@ -8,8 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### :warning: Major enhancements
 
 * Samplesheet format has changed from `group,replicate,fastq_1,fastq_2,strandedness` to `sample,fastq_1,fastq_2,strandedness`
-  * This gives users the flexibility to name their samples however they wish (see [#550](https://github.com/nf-core/rnaseq/issues/550]))
-  * PCA generated by DESeq2 will now be monochrome and will not be grouped by using the replicate id
+    * This gives users the flexibility to name their samples however they wish (see [#550](https://github.com/nf-core/rnaseq/issues/550]))
+    * PCA generated by DESeq2 will now be monochrome and will not be grouped by using the replicate id
 * Updated Nextflow version to `v21.04.0` (see [nextflow#572](https://github.com/nextflow-io/nextflow/issues/1964))
 * Restructure pipeline scripts into `modules/`, `subworkflows/` and `workflows/` directories
 
@@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [[#604](https://github.com/nf-core/rnaseq/issues/604)] - Additional fasta with GENCODE annotation results in biotype error
 * [[#610](https://github.com/nf-core/rnaseq/issues/610)] - save R objects as RDS
 * [[#619](https://github.com/nf-core/rnaseq/issues/619)] - implicit declaration of the workflow in main
+* [[#629](https://github.com/nf-core/modules/pull/629)] - Add and fix EditorConfig linting in entire pipeline
 * [[nf-core/modules#423](https://github.com/nf-core/modules/pull/423)] - Replace `publish_by_id` module option to `publish_by_meta`
 * [[nextflow#2060](https://github.com/nextflow-io/nextflow/issues/2060)] - Pipeline execution hang when native task fail to be submitted
 
@@ -50,9 +51,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 |                             | `--validate_params`            |
 | `--clusterOptions`          |                                |
 
-> **NB:** Parameter has been __updated__ if both old and new parameter information is present.  
-> **NB:** Parameter has been __added__ if just the new parameter information is present.  
-> **NB:** Parameter has been __removed__ if parameter information isn't present.  
+> **NB:** Parameter has been __updated__ if both old and new parameter information is present.
+> **NB:** Parameter has been __added__ if just the new parameter information is present.
+> **NB:** Parameter has been __removed__ if parameter information isn't present.
 
 ### Software dependencies
 
@@ -64,20 +65,20 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `multiqc`   | 1.9         | 1.10.1      |
 | `preseq`    | 2.0.3       | 3.1.2       |
 
-> **NB:** Dependency has been __updated__ if both old and new version information is present.  
-> **NB:** Dependency has been __added__ if just the new version information is present.  
-> **NB:** Dependency has been __removed__ if version information isn't present.  
+> **NB:** Dependency has been __updated__ if both old and new version information is present.
+> **NB:** Dependency has been __added__ if just the new version information is present.
+> **NB:** Dependency has been __removed__ if version information isn't present.
 
 ## [[3.0](https://github.com/nf-core/rnaseq/releases/tag/3.0)] - 2020-12-15
 
 ### :warning: Major enhancements
 
 * You will need to install Nextflow `>=20.11.0-edge` to run the pipeline. If you are using Singularity, then features introduced in that release now enable the pipeline to directly download Singularity images hosted by Biocontainers as opposed to performing a conversion from Docker images (see [#496](https://github.com/nf-core/rnaseq/issues/496)).
 * The previous default of aligning BAM files using STAR and quantifying using featureCounts (`--aligner star`) has been removed. The new default is to align with STAR and quantify using Salmon (`--aligner star_salmon`).
-  * This decision was made primarily because of the limitations of featureCounts to appropriately quantify gene expression data. Please see [Zhao et al., 2015](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001) and [Soneson et al., 2015](https://f1000research.com/articles/4-1521/v1)).
+    * This decision was made primarily because of the limitations of featureCounts to appropriately quantify gene expression data. Please see [Zhao et al., 2015](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001) and [Soneson et al., 2015](https://f1000research.com/articles/4-1521/v1)).
 * For similar reasons, **quantification will not be performed** if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments.
-  * This pipeline option is still available for those who have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2. No gene-level quantification results will be generated.
-  * In a future release we hope to add back quantitation for HISAT2 using different tools.
+    * This pipeline option is still available for those who have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2. No gene-level quantification results will be generated.
+    * In a future release we hope to add back quantitation for HISAT2 using different tools.
 
 ### Enhancements & fixes
 
@@ -108,9 +109,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 |                              | `--singularity_pull_docker_container` |
 | `--skip_featurecounts`       |                                       |
 
-> **NB:** Parameter has been __updated__ if both old and new parameter information is present.  
-> **NB:** Parameter has been __added__ if just the new parameter information is present.  
-> **NB:** Parameter has been __removed__ if parameter information isn't present.  
+> **NB:** Parameter has been __updated__ if both old and new parameter information is present.
+> **NB:** Parameter has been __added__ if just the new parameter information is present.
+> **NB:** Parameter has been __removed__ if parameter information isn't present.
 
 ### Software dependencies
 
@@ -126,9 +127,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `ucsc-bedclip`                      |             | 377         |
 | `umi_tools`                         | 1.0.1       | 1.1.1       |
 
-> **NB:** Dependency has been __updated__ if both old and new version information is present.  
-> **NB:** Dependency has been __added__ if just the new version information is present.  
-> **NB:** Dependency has been __removed__ if version information isn't present.  
+> **NB:** Dependency has been __updated__ if both old and new version information is present.
+> **NB:** Dependency has been __added__ if just the new version information is present.
+> **NB:** Dependency has been __removed__ if version information isn't present.
 
 ## [[2.0](https://github.com/nf-core/rnaseq/releases/tag/2.0)] - 2020-11-12
 
@@ -244,10 +245,10 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 * `--skipEdgeR` qc not performed by DESeq2 instead
 * `--star_memory` in favour of updating centrally on nf-core/modules if required
 * Strandedness is now specified at the sample-level via the input samplesheet
-  * `--forwardStranded`
-  * `--reverseStranded`
-  * `--unStranded`
-  * `--pico`
+    * `--forwardStranded`
+    * `--reverseStranded`
+    * `--unStranded`
+    * `--pico`
 
 ### Software dependencies
 
@@ -292,9 +293,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `r-gplots`                          | -           | -           |
 | `r-markdown`                        | -           | -           |
 
-> **NB:** Dependency has been __updated__ if both old and new version information is present.  
-> **NB:** Dependency has been __added__ if just the new version information is present.  
-> **NB:** Dependency has been __removed__ if version information isn't present.  
+> **NB:** Dependency has been __updated__ if both old and new version information is present.
+> **NB:** Dependency has been __added__ if just the new version information is present.
+> **NB:** Dependency has been __removed__ if version information isn't present.
 
 ## [[1.4.2](https://github.com/nf-core/rnaseq/releases/tag/1.4.2)] - 2019-10-18
 
@@ -321,9 +322,9 @@ Major novel changes include:
 * Several improvements in `featureCounts` handling of types other than `exon`. It is possible now to handle nuclearRNAseq data. Nuclear RNA has un-spliced RNA, and the whole transcript, including the introns, needs to be counted, e.g. by specifying `--fc_count_type transcript`.
 * Support for [outputting unaligned data](https://github.com/nf-core/rnaseq/issues/277) to results folders.
 * Added options to skip several steps
-  * Skip trimming using `--skipTrimming`
-  * Skip BiotypeQC using `--skipBiotypeQC`
-  * Skip Alignment using `--skipAlignment` to only use pseudo-alignment using Salmon
+    * Skip trimming using `--skipTrimming`
+    * Skip BiotypeQC using `--skipBiotypeQC`
+    * Skip Alignment using `--skipAlignment` to only use pseudo-alignment using Salmon
 
 ### Documentation updates
 
@@ -434,7 +435,7 @@ Major novel changes include:
 * Remove legacy rseqc `strandRule` config code. [#119](https://github.com/nf-core/rnaseq/issues/119)
 * Added STRINGTIE ballgown output to results folder [#125](https://github.com/nf-core/rnaseq/issues/125)
 * HiSAT index build now requests `200GB` memory, enough to use the exons / splice junction option for building.
-  * Added documentation about the `--hisatBuildMemory` option.
+    * Added documentation about the `--hisatBuildMemory` option.
 * BAM indices are stored and re-used between processes [#71](https://github.com/nf-core/rnaseq/issues/71)
 
 ### Bug Fixes
@@ -474,25 +475,25 @@ In summary, the main changes are:
 * Rebranding and renaming throughout the pipeline to nf-core
 * Updating many parts of the pipeline config and style to meet nf-core standards
 * Support for GFF files in addition to GTF files
-  * Just use `--gff` instead of `--gtf` when specifying a file path
+    * Just use `--gff` instead of `--gtf` when specifying a file path
 * New command line options to skip various quality control steps
 * More safety checks when launching a pipeline
-  * Several new sanity checks - for example, that the specified reference genome exists
+    * Several new sanity checks - for example, that the specified reference genome exists
 * Improved performance with memory usage (especially STAR and Picard)
 * New BigWig file outputs for plotting coverage across the genome
 * Refactored gene body coverage calculation, now much faster and using much less memory
 * Bugfixes in the MultiQC process to avoid edge cases where it wouldn't run
 * MultiQC report now automatically attached to the email sent when the pipeline completes
 * New testing method, with data on GitHub
-  * Now run pipeline with `-profile test` instead of using bash scripts
+    * Now run pipeline with `-profile test` instead of using bash scripts
 * Rewritten continuous integration tests with Travis CI
 * New explicit support for Singularity containers
 * Improved MultiQC support for DupRadar and featureCounts
-  * Now works for all users instead of just NGI Stockholm
+    * Now works for all users instead of just NGI Stockholm
 * New configuration for use on AWS batch
 * Updated config syntax to support latest versions of Nextflow
 * Built-in support for a number of new local HPC systems
-  * CCGA, GIS, UCT HEX, updates to UPPMAX, CFC, BINAC, Hebbe, c3se
+    * CCGA, GIS, UCT HEX, updates to UPPMAX, CFC, BINAC, Hebbe, c3se
 * Slightly improved documentation (more updates to come)
 * Updated software packages