Merge pull request #499 from MaxUlysse/1.2.5

Preparing release 1.2.5

.github/CONTRIBUTING.md

@@ -0,0 +1,25 @@
+# CAW Contributing Guidelines
+
+Hi there! Many thanks for taking an interest in improving CAW.
+
+We try to manage the required tasks for CAW using GitHub issues, you probably came to this page when creating one. Please use the prefilled template to save time.
+
+However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)
+
+> If you need help using CAW then the best place to go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/SciLifeLab/CAW
+
+## Contribution workflow
+If you'd like to write some code for CAW, the standard workflow
+is as follows:
+
+1. Check that there isn't already an issue about your idea in the
+   [CAW issues](https://github.com/SciLifeLab/CAW/issues) to avoid
+   duplicating work.
+    * Feel free to add a new issue here for the same reason.
+2. Fork the CAW repository to your GitHub account
+3. Make the necessary changes / additions within your forked repository
+4. Submit a Pull Request against the master 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 [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
+
+For further information/help, please consult the [CAW documentation](https://github.com/SciLifeLab/CAW#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/SciLifeLab/CAW) or contact us: [email protected], [email protected]

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,43 @@
+<!--
+Hi there!
+
+Many thanks for creating a CAW issue.
+
+Most issues fall into two categories: either you're reporting a problem with CAW or you'd like a change/improvement.
+
+To make sure that you include all of the information needed, please use the template below, you can delete what is not needed.
+
+Please try to include all you can.
+
+You can also delete this entire thing and just type :)
+-->
+
+## Expected Behavior
+<!--
+If you're describing a bug, tell us what should happen
+If you're suggesting a change/improvement, tell us how you think it should work
+-->
+
+## Current Behavior
+<!---
+If describing a bug, tell us what actually happened
+If suggesting a change/improvement, explain the difference from current behavior
+-->
+
+## Possible Solution
+<!---
+Not obligatory, but suggest a fix/reason for the bug,
+or ideas how to implement the addition or change
+-->
+
+## Context (for bugs)
+<!---
+Providing context helps us coming up with a solution
+Include as many relevant details about the environment you experienced the bug in
+-->
+- **CAW `nextflow.log`:**
+  <!-- Re-execute the command line that resulted in a bug with --verbose and -resume and join the .nextflow.log -->
+  - [please drag and drop the `.nextflow.log` file that will help understand the error here]
+- **CAW `input.TSV`:**
+  <!-- Anonymize your TSV file if necessary and join it too  -->
+  - [please drag and drop the `TSV` file that will help reproduce or understand the error here]

.github/RELEASE_CHECKLIST.md

@@ -0,0 +1,21 @@
+# Release checklist
+This checklist is for our own reference
+
+1. Check that everything is up to date and ready to go
+2. Increase version numbers.
+3. Update version numbers in code: `main.nf`, `buildContainers.nf`, `buildReferences.nf`
+4. If any changes on any containers, match the tag to current version `docker.config`, `singularity.config`, `singularity-path.config`.
+5. Build, and get the containers.
+  - `./scripts/do_all.sh --push`
+  - `./scripts/do_all.sh --pull`
+6. Test against sample data.
+  - Check for any command line errors
+  - Check version numbers are printed correctly
+  - `./scripts/test.sh -p docker`
+  - `./scripts/test.sh -p singularity`
+  - `./scripts/test.sh -p singularityPath`
+7. Commit and push version updates
+8. Make a [release](https://github.com/SciLifeLab/CAW/releases) on GitHub - list PRs as changelog.
+9. Tweet that new version is released
+10. Commit and push. Continue making more awesome :metal:
+11. Have fika :cake:

.gitignore

@@ -9,5 +9,6 @@ work/
 .nextflow*
 *.img
 *.tar.gz
+report.html*
 timeline.html*
 trace.txt*

.travis.yml

@@ -8,19 +8,19 @@ services:
   - docker
 
 env:
-  - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
-  - NXF_VER=0.25.6 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
-  - NXF_VER=0.25.6 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
-  - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=RECALIBRATE TOOL_INSTALL=all
-  - NXF_VER=0.25.6 PROFILE=docker TEST=RECALIBRATE TOOL_INSTALL=nextflow
-  - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=REALIGN TOOL_INSTALL=all
-  - NXF_VER=0.25.6 PROFILE=docker TEST=REALIGN TOOL_INSTALL=nextflow
-  - NXF_VER=0.25.6 PROFILE=docker TEST=BUILDCONTAINERS TOOL_INSTALL=nextflow
-  - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=MAPPING TOOL_INSTALL=all
-  - NXF_VER=0.25.6 PROFILE=docker TEST=MAPPING TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=RECALIBRATE TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=RECALIBRATE TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=REALIGN TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=REALIGN TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 PROFILE=docker TEST=BUILDCONTAINERS TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=MAPPING TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=MAPPING TOOL_INSTALL=nextflow
 
 install: # Install Nextflow (and Singularity if needed)
   - "./scripts/install.sh --tool $TOOL_INSTALL"
 
 script:
-  - "./scripts/test.sh --profile $PROFILE --test $TEST"
+  - "travis_wait 50 ./scripts/test.sh --profile $PROFILE --test $TEST"

README.md

@@ -8,11 +8,19 @@ CAW is a complete open source pipeline to detect somatic variants from WGS data
 
 The pipeline uses [Nextflow][nextflow-link], a bioinformatics domain specific language for workflow building and [Singularity](http://singularity.lbl.gov/), a container technology specific for high-performance computing.
 
-This pipeline is primarily used with cluster on the Swedish [UPPMAX systems](https://www.uppmax.uu.se/). However, the pipeline should be able to run on any system that supports Nextflow. The pipeline comes with some configuration for different systems. See the [documentation](#documentation) for more information.
+This pipeline is primarily used with cluster on the Swedish [UPPMAX systems](https://www.uppmax.uu.se/).
+However, the pipeline should be able to run on any system that supports Nextflow.
+The pipeline comes with some configuration for different systems.
+See the [documentation](#documentation) for more information.
 
-We utilize [GATK best practices](https://software.broadinstitute.org/gatk/best-practices/) to align, realign and recalibrate short-read data in parallel for both normal and tumor sample. After these preprocessing steps, several somatic variant callers scan the resulting BAM files: [MuTect1][mutect1-link], [MuTect2][gatk-link] and [Strelka][strelka-link] are used to find somatic SNVs and small indels, also [GATK HaplotyeCaller][gatk-link] for both the normal and the tumor sample. For structural variants we use [Manta][manta-link]. Furthermore, we are applying [ASCAT][ascat-link] to estimate sample heterogeneity, ploidy and CNVs.
+Caw is based on [GATK best practices](https://software.broadinstitute.org/gatk/best-practices/) to align, realign and recalibrate short-read data in parallel for both normal and tumor sample.
+After these preprocessing steps, several somatic variant callers scan the resulting BAM files: [MuTect1][mutect1-link], [MuTect2][gatk-link], [Freebayes][freebayes-link] and [Strelka][strelka-link] are used to find somatic SNVs and small indels, also [GATK HaplotyeCaller][gatk-link] for both the normal and the tumor sample.
+For structural variants we use [Manta][manta-link].
+Furthermore, we are applying [ASCAT][ascat-link] to estimate sample heterogeneity, ploidy and CNVs.
 
-The pipeline can begin the analysis either from raw FASTQ files, only from the realignment step, or directly with any subset of variant callers using recalibrated BAM files. At the end of the analysis the resulting VCF files are merged to facilitate further downstream processing, though results from each caller are also retained. The flow is capable of accommodating additional variant calling software or CNV callers. It is also prepared to process normal, tumor and several relapse samples.
+The pipeline can begin the analysis either from raw FASTQ files, only from the realignment step, or directly with any subset of variant callers using recalibrated BAM files.
+At the end of the analysis the resulting VCF files are merged to facilitate further downstream processing, though results from each caller are also retained.
+The flow is capable of accommodating additional variant calling software or CNV callers. It is also prepared to process normal, tumor and several relapse samples.
 
 Besides variant calls, the workflow provides quality controls presented by [MultiQC][multiqc-link].
 
@@ -40,7 +48,10 @@ The CAW pipeline comes with documentation about the pipeline, found in the `doc/
 14. [More information about ASCAT](doc/ASCAT.md)
 15. [Folder structure](doc/FOLDER.md)
 
-For further information/help contact: [email protected], [email protected] or join the gitter chat: [gitter.im/SciLifeLab/CAW][gitter-link].
+## Contributions & Support
+
+- [Contributions guidelines](.github/CONTRIBUTING.md)
+For further information/help, don't hesitate to get in touch on [Gitter][gitter-link] or contact us: [email protected], [email protected]
 
 ## Authors
 
@@ -63,6 +74,7 @@ For further information/help contact: [email protected], szilveszter.j
 
 [ascat-link]: https://github.com/Crick-CancerGenomics/ascat
 [caw-site-link]: http://opensource.scilifelab.se/projects/caw/
+[freebayes-link]: https://github.com/ekg/freebayes
 [gatk-link]: https://github.com/broadgsa/gatk-protected
 [gitter-badge]: https://badges.gitter.im/SciLifeLab/CAW.svg
 [gitter-link]: https://gitter.im/SciLifeLab/CAW
@@ -76,7 +88,7 @@ For further information/help contact: [email protected], szilveszter.j
 [nextflow-link]: https://www.nextflow.io/
 [ngi-link]: https://ngisweden.scilifelab.se/
 [scilifelab-link]: https://www.scilifelab.se/
-[scilifelab-stockholm-link]: https://www.scilifelab.se/platforms/ngi/
+[scilifelab-stockholm-link]: https://www.scilifelab.se/facilities/ngi-stockholm/
 [strelka-link]: https://github.com/Illumina/strelka
 [travis-badge]: https://api.travis-ci.org/SciLifeLab/CAW.svg
 [travis-link]: https://travis-ci.org/SciLifeLab/CAW