grape-nf - Version 1.3.1

• Use annotation file object as input for tasks - fix #84 [5ce9bde]

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.3.0...v1.3.1

- Nextflow
Published by emi80 over 1 year ago

grape-nf - Version 1.3.0

• Reduce memory usage in RSEM quantification process [78fd890]
• Fix regression - allow usage of precomputed genome index [4a885e3]
• Minor changes to main pipeline script [a41b5dc]
• Fix issue with contig step on unstranded data [87d7db7]
• Fix file issue in fastaIndex process [36f3469]
• Update memory for mapping [e00579a]
• Fix file issues in steps for mapping and quantification indices [574a115]
• Fix syntax errors in rsem module [a7b549e]
• Refactor modules and workflows [df1731f]

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.2.1...v1.3.0

- Nextflow
Published by emi80 about 2 years ago

grape-nf - Version 1.1.5

• Reduce memory usage in RSEM quantification process

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.1.4...v1.1.5

- Nextflow
Published by emi80 over 2 years ago

grape-nf - Version 1.2.1

• Update numeric type for memory in mapping module - fix regression

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.2...v1.2.1

- Nextflow
Published by emi80 over 2 years ago

grape-nf - Version 1.2

• Add CFF file for citattion - resolve #75
• Update ci script and GH actions workflow
• Skip QC downstream steps for bams with no alignments - fix #76
• Add sample information in process tags - resolve #73
• Correct reported number of sequencing runs for non-unique ids - fix #74
• Update trace file path in main config
• DSL2 refactoring - #78 #62

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.1.4...v1.2

- Nextflow
Published by emi80 over 2 years ago

grape-nf - Version 1.1.4

• Update cross key to get bamFilesToTranscriptome and bamStatsFiles - fixes #72

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.1.3...v1.1.4

- Nextflow
Published by emi80 almost 3 years ago

grape-nf - Version 1.1.3

• Handle other == NA in infer experiment script - fix #71

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.1.2...v1.1.3

- Nextflow
Published by emi80 almost 3 years ago

grape-nf - Version 1.1.2

• Update numeric type for mapping memory - fixes #70

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.1.1...v1.1.2

- Nextflow
Published by emi80 almost 3 years ago

grape-nf - Version 1.1.1

• Set memory limit to STAR index process - fix #66

Additional improvements and fixes:

• Update GitHub workflow
• Merge pull request #61 from guigolab/dependabot/bundler/docs/addressable-2.8.0
• Bump addressable from 2.4.0 to 2.8.0 in /docs

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.1.1...v1.1.0

- Nextflow
Published by emi80 over 3 years ago

grape-nf - Version 1.1.0

• Add output files section in readme - #58
• Change quantification process view - #59

Additional improvements and fixes:

• Switch CI to GitHub Actions
• Fix issue with sambamba repo checkout in Dockerfile

Full Changelog: https://github.com/guigolab/grape-nf/compare/v1.0.0...v1.1.0

- Nextflow
Published by emi80 almost 5 years ago

grape-nf - Version 1.0.0

First IHEC release

• Whole pipeline refactoring - #51
• Fix wrong merging information - #55
• Add ability to use regex for reference prefix in bigwig step - #17

Additional improvements and fixes:

• Use 2/3 of the process memory in mapping
• Increase quantification memory in IHEC resources config file
• Update sambamba version to 0.7.1
• Update bamstats version to 0.3.4
• Enable autoMounts for Singularity by default
• Add script to prepare input FASTQ files from BAM files
• Fix issue in field order when reading input BAMs
• Add gtf and gff to supported file types in CI script
• Sort transcriptome BAMs before merge
• Remove test.sh, update CI tests and TravisCI configuration file
• Fix workflow for input BAMs and add test profile
• Add threshold option to infer experiment script and add corresponding pipeline parameter
• Fix read group attributes in mapping

IHEC specific changes:

• Move all IHEC documentation to ihec-setup.md, update and clean up
• Clean up pipeline config and use single IHEC image for the IHEC profile
• Add script to pre-fetch the IHEC Singularity image
• Add the IHEC profile to TravisCI config
• Update test data and checksum, add checksums for the IHEC profile

Full Changelog: https://github.com/guigolab/grape-nf/compare/v0.4.1...v1.0.0

- Nextflow
Published by emi80 over 5 years ago

grape-nf - Version 0.4.1

• Fix wrong comment in config file breaking pipeline execution
• Update minimum Nextflow version badge in readme to 0.30.2

Full Changelog: https://github.com/guigolab/grape-nf/compare/v0.4.0...v0.4.1

- Nextflow
Published by emi80 over 6 years ago

grape-nf - 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

Full Changelog: https://github.com/guigolab/grape-nf/compare/v0.3.0...v0.4.0

- Nextflow
Published by emi80 over 6 years ago

grape-nf - 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

Full Changelog: https://github.com/guigolab/grape-nf/compare/v0.2.1...v0.3.0

- Nextflow
Published by emi80 over 6 years ago

grape-nf - Version 0.2.1

• Decreasing disk stress and processing time of the contig step by replacing temporary bam files by pipes (thanks to @karl616)
• Add options for docker so that created files are no longer owned by root (thanks to @leshaker)

Full Changelog: https://github.com/guigolab/grape-nf/compare/v0.2.0...v0.2.1

- Nextflow
Published by emi80 over 8 years ago

grape-nf - Version 0.1.0

First version

Full Changelog: https://github.com/guigolab/grape-nf/commits/v0.1.0

- Nextflow
Published by emi80 over 8 years ago

grape-nf - 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

Full Changelog: https://github.com/guigolab/grape-nf/compare/v0.1.0...v0.2.0

- Nextflow
Published by emi80 over 8 years ago