Dev -> Master for v3.6 release

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,4 +1,3 @@
-
 name: Bug report
 description: Report something that is broken or incorrect
 labels: bug

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
     - [ ] 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`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/awsfulltest.yml

@@ -32,4 +32,6 @@ jobs:
               "aligner": "${{ matrix.aligner }}"
             }
           profiles: test_full,aws_tower
-          pre_run_script: 'export NXF_VER=21.10.3'
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/awstest.yml

@@ -25,4 +25,6 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-          pre_run_script: 'export NXF_VER=21.10.3'
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/branch.yml

@@ -43,4 +43,3 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-

.github/workflows/ci.yml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
@@ -76,7 +76,7 @@ jobs:
 
       - name: Run pipeline with STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
@@ -98,7 +98,7 @@ jobs:
 
       - name: Run pipeline with RSEM STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
 
   hisat2:
     name: Test HISAT2 with workflow parameters
@@ -120,7 +120,7 @@ jobs:
 
       - name: Run pipeline with HISAT2 and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
 
   salmon:
     name: Test Salmon with workflow parameters
@@ -142,4 +142,4 @@ jobs:
 
       - name: Run pipeline with Salmon and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results

.github/workflows/linting.yml

@@ -12,9 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
@@ -51,9 +49,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -65,13 +61,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.yamllint.yml
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -87,7 +81,7 @@ jobs:
             * Install `yaml-lint`
                 * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
             * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
                 * Fix any reported errors in your YAML files
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
@@ -142,4 +136,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-

.github/workflows/linting_comment.yml

@@ -1,4 +1,3 @@
-
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -27,4 +26,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-

.gitpod.yml

@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore                 # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow                 # Highlight indentation level
+    - streetsidesoftware.code-spell-checker  # Spelling checker for source code

.nf-core.yml

@@ -3,13 +3,19 @@ lint:
     - assets/email_template.html
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - lib/NfcoreSchema.groovy
 update:
   nf-core/modules:
-    rseqc/bamstat: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/inferexperiment: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/innerdistance: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/junctionannotation: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/junctionsaturation: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/readdistribution: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/readduplication: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/tin: "ce8c781bb494c2cc1f0a951c31c7b2f4af12e8af"
+    rseqc/bamstat: "e745e167c1020928ef20ea1397b6b4d230681b4d"
+    rseqc/inferexperiment: "e745e167c1020928ef20ea1397b6b4d230681b4d"
+    rseqc/innerdistance: "e745e167c1020928ef20ea1397b6b4d230681b4d"
+    rseqc/junctionannotation: "e745e167c1020928ef20ea1397b6b4d230681b4d"
+    rseqc/junctionsaturation: "e745e167c1020928ef20ea1397b6b4d230681b4d"
+    rseqc/readdistribution: "e745e167c1020928ef20ea1397b6b4d230681b4d"
+    rseqc/readduplication: "e745e167c1020928ef20ea1397b6b4d230681b4d"
+    rseqc/tin: "4dbc166a7c30e963511fb5c9870fbcaa158a53a9"

.yamllint.yml

@@ -0,0 +1,5 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable

CHANGELOG.md

@@ -3,6 +3,34 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.6](https://github.com/nf-core/rnaseq/releases/tag/3.6)] - 2022-03-01
+
+### Enhancements & fixes
+
+* [nf-core/tools#1415](https://github.com/nf-core/tools/issues/1415) - Make `--outdir` a mandatory parameter
+* [[#734](https://github.com/nf-core/rnaseq/issues/734)] - Is a vulnerable picard still used ? log4j vulnerability
+* [[#744](https://github.com/nf-core/rnaseq/issues/744)] - Auto-detect and raise error if CSI is required for BAM indexing
+* [[#750](https://github.com/nf-core/rnaseq/issues/750)] - Optionally ignore R1 / R2 after UMI extraction process
+* [[#752](https://github.com/nf-core/rnaseq/issues/752)] - How to set publishing mode for all processes?
+* [[#753](https://github.com/nf-core/rnaseq/issues/753)] - Add warning when user provides `--transcript_fasta`
+* [[#754](https://github.com/nf-core/rnaseq/issues/754)] - DESeq2 QC issue linked to `--count_col` parameter
+* [[#755](https://github.com/nf-core/rnaseq/issues/755)] - Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS process
+* [[#759](https://github.com/nf-core/rnaseq/issues/759)] - Empty lines in samplesheet.csv cause a crash
+* [[#769](https://github.com/nf-core/rnaseq/issues/769)] - Do not run RSeQC tin.py by default
+
+### Parameters
+
+| Old parameter                 | New parameter                         |
+|-------------------------------|---------------------------------------|
+|                               | `--publish_dir_mode`                  |
+|                               | `--umi_discard_read`                  |
+
+> **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 new parameter information isn't present.
+
 ## [[3.5](https://github.com/nf-core/rnaseq/releases/tag/3.5)] - 2021-12-17
 
 ### Enhancements & fixes
@@ -18,8 +46,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [[#727](https://github.com/nf-core/rnaseq/issues/727)] - Fix transcriptome staging issues on DNAnexus for rsem/prepareference
 * [[#728](https://github.com/nf-core/rnaseq/issues/728)] - Add RSeQC TIN.py as a quality metric for the pipeline
 
-### Parameters
-
 ## [[3.4](https://github.com/nf-core/rnaseq/releases/tag/3.4)] - 2021-10-05
 
 ### Enhancements & fixes
@@ -42,9 +68,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 |                             | `--save_bbsplit_reads`         |
 |                             | `--skip_bbsplit`               |
 
-> **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
 
@@ -60,9 +86,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `sortmerna`   | 4.2.0       | 4.3.4       |
 | `trim-galore` | 0.6.6       | 0.6.7       |
 
-> **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.
 
 ## [[3.3](https://github.com/nf-core/rnaseq/releases/tag/3.3)] - 2021-07-29
 
@@ -83,9 +109,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `stringtie` | 2.1.4       | 2.1.7       |
 | `umi_tools` | 1.1.1       | 1.1.2       |
 
-> **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.
 
 ## [[3.2](https://github.com/nf-core/rnaseq/releases/tag/3.2)] - 2021-06-18
 
@@ -108,9 +134,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `--skip_sra_fastq_download` |                                |
 |                             | `--salmon_quant_libtype`       |
 
-> **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.
 
 ## [[3.1](https://github.com/nf-core/rnaseq/releases/tag/3.1)] - 2021-05-13
 
@@ -161,9 +187,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 |                             | `--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
 
@@ -175,9 +201,9 @@ 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
 
@@ -219,9 +245,9 @@ 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
 
@@ -237,9 +263,9 @@ 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
 
@@ -403,9 +429,9 @@ 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