Fix merge conflicts

.github/CONTRIBUTING.md

@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/rnaseq, the standard workflow is as
     * If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/rnaseq repository](https://github.com/nf-core/rnaseq) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build .` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -69,7 +69,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
+5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
 6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
 7. Add sanity checks for all relevant parameters.
 8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
@@ -83,7 +83,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
+Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
 - [ ] 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.
-- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] 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.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/linting.yml

@@ -53,7 +53,7 @@ jobs:
 
       - uses: actions/setup-node@v1
         with:
-          node-version: "10"
+          node-version: '10'
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker

.nf-core.yml

@@ -3,6 +3,17 @@ lint:
     - .markdownlint.yml
     - assets/email_template.html
     - assets/email_template.txt
-    - bin/scrape_software_versions.py
     - lib/NfcoreTemplate.groovy
     - assets/multiqc_config.yaml
+update:
+  nf-core/modules:
+    rseqc/bamstat: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    rseqc/inferexperiment: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    rseqc/innerdistance: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    rseqc/junctionannotation: "5dd049047d01e72c01a519422f17e203bca343ac"
+    rseqc/junctionsaturation: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    rseqc/readdistribution: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    rseqc/readduplication: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    sortmerna: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    star/align: "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+    star/genomegenerate: "e937c7950af70930d1f34bb961403d9d2aa81c7d"

CHANGELOG.md

@@ -3,11 +3,11 @@
 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).
 
-## [[3.3](https://github.com/nf-core/rnaseq/releases/tag/3.3)] - 2021-07-26
+## [[3.3](https://github.com/nf-core/rnaseq/releases/tag/3.3)] - 2021-07-28
 
 ### Enhancements & fixes
 
-* Updated pipeline template to [nf-core/tools 2.0.1](https://github.com/nf-core/tools/releases/tag/2.0.1)
+* Updated pipeline template to [nf-core/tools 2.1](https://github.com/nf-core/tools/releases/tag/2.1)
 * [[#668](https://github.com/nf-core/rnaseq/issues/668)] - Salmon quant with UMI-tools does not work
 * [[#674](https://github.com/nf-core/rnaseq/issues/674)] - Launch pipeline regex fails
 
@@ -17,9 +17,9 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 
 | Dependency  | Old version | New version |
 |-------------|-------------|-------------|
-| `umi_tools` | 1.1.1       | 1.1.2       |
 | `samtools`  | 1.10        | 1.12        |
 | `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.

README.md

@@ -54,7 +54,7 @@ The SRA download functionality has been removed from the pipeline (`>=3.2`) and
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`).
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`)
 
 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))_. Note: This pipeline does not currently support running with Conda on macOS if the `--remove_ribo_rna` parameter is used because the latest version of the SortMeRNA package is not available for this platform.
 

nextflow_schema.json

@@ -686,4 +686,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}