Merge pull request #1 from guigolab/IHEC

pre-release v1

.gitignore

@@ -3,5 +3,11 @@
 .nextflow*
 *.log
 *.db
+trace.txt*
 work/
 tmp/
+nextflow
+pipeline.db
+checksum/
+singularity/
+download/

.travis.yml

@@ -0,0 +1,20 @@
+dist: trusty
+sudo: required
+
+services:
+  - docker
+
+language: java
+
+jdk:
+  - oraclejdk8
+
+env:
+  - PROFILE=gemflux
+  - PROFILE=starrsem
+  - PROFILE=starflux
+  - PROFILE=markdup
+  - PROFILE=rmdup
+
+script:
+  - ./test.sh

CHANGELOG.md

@@ -0,0 +1,80 @@
+# GRAPE-nf Changelog
+
+## Version 0.4.1
+
+- Fix wrong comment in config file braking pipeline execution
+- Update minimum Nextflow version badge in readme to 0.30.2
+
+## Version 0.4.0
+
+- Add mark-duplicates step - #40.
+- Convert existing samtools commands in templates to corresponding available sambamba one - #41.
+- Add bamStats process - #42
+- Add process and logic to download input files - #43
+- Support compressed reference files - #44
+- Replace groupBy related logic in pipeline script - #46
+
+Additional fixes and improvements
+
+- Add memory limit to sambamba sort command in RSEM quantification step
+- Add sort buffer size option in sambamba markdup
+- Update container for fetch process
+- Update IHEC profile BAM sorting tool
+- Update Nextflow and TravisCI config files
+- Update gem mapping templates for new version of samtools
+- Add nextflow config profiles for IHEC and update TravisCI configuration
+- Clean-up into calls using closure syntax
+- Set halfCpus as integer and fix it when task.cpus is 1
+- Add Dockerfiles
+- Update readme and add description of pipeline parameters
+- Add Singularity section to readme with tips and troubleshoot
+- Update tool versions in readme
+- Bump sambamba version to 0.7.0
+- Bump tool versions for bamstats, samtools and RSeQC
+
+## Version 0.3.0
+
+- Fix #21 - sort index file lines when grouping paired `FASTQ` files
+- Disable Docker by default and update test script - resolve #22
+- Update test profiles and main config - address #25
+- Move process resource to external config file - #24
+- Modified quantification step by removing the temporary sorted bam file. By doing this we can pipe an uncompressed sam file directly to rsem   - #26 thanks @karl616
+- Fix issue with modified quantification templates - introduced by #26
+- Use withName process selector in configuration files - close #39
+- Update test script, configuration profiles and checksums - #30
+- Add option to enforce strandness - first implementation of #11
+- Fix bedgraph filename error in contig template - close #27
+- Add tool versions to readme - close #18
+
+Additional fixes and imporvements:
+
+- Change `README` markup to Markdown
+- Update CI configuration
+- Improve `RGCRG` bigwig templates by removing temporary bam files
+- Fix missing `NH:1` filter in contigs antisense template
+- Move to Travis CI
+- Fix issue with test script using wrong pipeline.db when running outside pipeline base dir
+
+
+## Version 0.2.1
+
+- Decreasing disk stress and processing time of the contig step by replacing temporary bam files by pipes. The drawback is that it is harder to control the maximum number of used cores.
+- Add options for docker so that created files are no longer owned by root
+
+## Version 0.2.0
+
+- Added ability to resolve relative paths in the index file against its current location
+- Change default profile to `starrsem`
+- Set bamSort to `samtools` in default profile
+- Fixed Empty lines in the index file result in a `ArrayIndexOutOfBoundsException` #7
+- Update documentation - resolve #6
+- Add genomeIndex parameter - fix #9
+- Add samtools index to mergeBam command template
+- Add mapping templates for `STAR 2.5`
+- Fix input BAMs considered as paired-end - resolve #14
+- Fix error when using both Genome and Transcriptome bams as inputs - fix #13
+- Enable trace by default in nextflow config
+
+## Version 0.1.0
+
+First version

Makefile

@@ -1,15 +1,19 @@
+.PHONY: changelog docs test clean-docs clean
+
+changelog:
+	@git log --pretty=%s $$(git describe --abbrev=0)..HEAD
+
 docs: docs/Makefile
 	@echo -n "== $$(tput setaf 3; tput bold)Updating GRAPE documentation...$$(tput sgr0)"
 	@$(MAKE) -C docs deploy
 	@echo "$$(tput setaf 2; tput bold)done$$(tput sgr0)"
 
 test: test.sh
-	@./test.sh
+	@PROFILE=testStarRsem ./test.sh
 
 clean-docs: docs/Makefile
 	@$(MAKE) -C docs clean
 
-clean-test:
+clean:
 	@rm -rf work nextflow .nextflow* checksum pipeline.db
-
-clean-all: clean-docs clean-test
+