Merge pull request #486 from apeltzer/dev

Add some launch docs

Author: jfy133

.github/CONTRIBUTING.md

@@ -18,8 +18,9 @@ If you'd like to write some code for nf-core/eager, the standard workflow is as
 1. Check that there isn't already an issue about your idea in the [nf-core/eager issues](https://github.com/nf-core/eager/issues) to avoid duplicating work
     * 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/eager repository](https://github.com/nf-core/eager) to your GitHub account
-3. Make the necessary changes / additions within your forked repository
-4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+3. Make the necessary changes / additions within your forked repository (following [code contribution guidelines](https://github.com/nf-core/eager/blob/dev/docs/code_contribution.md))
+4. Use `nf-core schema build .` and add any new parameters to the pipeline JSON schema (requires 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/).
 

CHANGELOG.md

@@ -11,14 +11,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 * **Major** Automated Cloud Tests with large-scale data on [AWS](https://aws.amazon.com/)
 * **Major** Re-wrote input logic to accept a TSV 'map' file in addition to direct paths to FASTQ
+* **Major** Added JSON Schema, enabling web GUI for configuration of pipeline
 * **Major** Lane and library merging implement
   * When using TSV input, one libraries with the multiple _lane_ will be merged together, before mapping
     * Strip FASTQ will also produce a lane merged 'raw' but 'stripped' FASTQ file
   * When using TSV input, one sample with multiple (same treatment) libraries will be merged together.
   * Important: direct FASTQ paths will not have this functionality. TSV is required.
 * [#40](https://github.com/nf-core/eager/issues/40) - Added the pileupCaller genotyper from [sequenceTools](https://github.com/stschiff/sequenceTools)
 * Added sanity check and clearer error message when `--fasta_index` is provided and filepath does not end in `.fai`.
-* Added basic json_schema
 * Improved error messages
 * Added ability for automated emails using `mailutils` to also send MultiQC reports
 * General documentation additions and cleaning, updated figures with CC-BY license

README.md

@@ -90,7 +90,7 @@ Additional functionality contained by the pipeline currently includes:
 
         nextflow run nf-core/eager -profile <docker/singularity/conda>,test
 
-5. Start running your own ancient DNA analysis!
+5. Start running your own ancient DNA analysis either via the command-line or [GUI](https://nf-co.re/launch)! Command line example:
 
         nextflow run nf-core/eager -profile <docker/singularity/conda> --input '*_R{1,2}.fastq.gz' --fasta '<your_reference>.fasta'
 

docs/usage.md

@@ -91,6 +91,8 @@ To see the the EAGER pipeline help message run: `nextflow run nf-core/eager --he
 
 > By default, if a pipeline step fails, nf-core/eager will resubmit the job with twice the amount of CPU and memory. This will occur two times before failing.
 
+If you want to configure your pipeline interactively using a graphical user interface, please visit [https://nf-co.re/launch](https://nf-co.re/launch), select the `eager` pipeline and the version you intend to run and follow the on-screen instructions to create a config for your pipeline run.
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: