Patch to fix software versions output

Main changes:

• Squid and pizzly are no longuer supported
• Removed --fusioninspector_filter and --fusionreport_filter in favor of --tools_cutoff (default = 1, no filters applied)
• Removed FusionGDB from fusion-report
• Improved vcf file creation, using --annotate --examine_coding_effect with fusioninspector to collect more data
• Removed harsh trimming option, fastp trimming still available
• Removed qualimap rna_seq

Bug fixes:

• building references is possible without a samplesheet
• Fix channel i/o issue in StringTie workflow
• Various fusion-report issues with download
• Improved CI

Changelog:

Changed

• Use institutional configs by default #381
• Remove redundant indexing in starfusion and qc workflows #387
• Output bai files in same directory as bam files #387
• Update and review documentation #396
• Update picard container for PICARD_COLLECTRNASEQMETRICS to 3.0.0 #395
• Renamed output files #395
  • Arriba visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation
  • cram file from output bam of STAR_FOR_ARRIBA: meta.id to meta.id_star_for_arriba
  • cram file from output bam of STAR_FOR_STARFUSION: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out
  • fusion-report index.html file to meta.id_fusionreport_index.html
  • meta.id.vcf output from MEGAFUSION to meta.id_fusion_data.vcf

Fixed

• Tail trimming for reverse reads #379
• Set html files as optional in fusionreport #380
• Provide gene count file by default when running STAR_FOR_STARFUSION #385
• Fix fusion-report issue with MACOXS directories #386
• The fusion lists is updated to contain two branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation #388
• Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases #403

Removed

• samtools sort and samtools index for arriba workflow were dispensable and were removed #395
• Removed trimmed fastqc report from multiqc #394

New Contributors

• @fevac made their first contribution in #379
• @efgstone made their first contribution in #382

Full Changelog: 2.3.4…2.4.0

Fix for megafusion

Fix for megafusion (again)

Fixes for megafusion

Changed permissions on megafusion script

Added

• Shell specification to bash
• COSMIC password put into quotes
• Trimmed reads QC in MultiQC
• Add ARRIBA_VISUALISATION to processed affected by --skip_vis
• Option fusionreport_filter to in/activate fusionreport displaying of fusions detected by 2 or more tools

Changed

• Arriba visualisation now runs for FusionInspector (combined tools) results, not only Arriba results
• Updated metro map with trimming options and placed Arriba visualisation after FusionInspector
• Exit with error when using squid in combination with any ensembl version different from 102

Fixed

• Channel issue with indexing of files with using --cram squid
• Arriba references published in the correct folder

Version 2.0.0 includes stringtie in --all, a fastp trimming option, fixed for arriba references among other (see details below).

Important: the references need to be rebuilt.

Check usage.md for how to use the new options.

Detailed CHANGELOG:

Added

• exitStatus 140 now part of the retry strategy
• stubs to all local modules
• --stringtie option added with StringTie v2.2.1 to detect splicing events. Not included in fusion-report or fusionInspector summaries. Included in the --all workflow
• Generation of ribosomal RNA interval list with build_references and use it in picard CollectRnaMetrics
• Add csv output to fusionreport
• Trimming workflow using fastp: use trimmed reads for all tools
• whitelist parameter to add custom fusions to the detected ones and consider the whole for the fusionInspector analysis
• Compression to CRAM files for arriba, squid and starfusion workflows (fusioncatcher and pizzly do not produce SAM/BAM files, fusioninspector BAM files are too small to benefit from compression)
• --qiagen option to download from QIAGEN instead of COSMIC (use QIAGEN user and password for cosmic_username and cosmic_passwd)
• Bumped STAR genomegenerate time request for building as it was always crashing for most users
• Fixed issue with arriba visualisation parameters #326

Changed

• Test profiles unified under ‘test’ but if the references do not all need to be downloaded, run with -stub
• Update CUSTOM_DUMPSOFTWAREVERSIONS to use multiqc version 1.13
• Updated to nf-core template 2.7.2, with all module updates
• MultiQC updated to 1.13a in process dumpsoftwareversion
• Patch fusion-report version with fixed mittelman DB and DB extraction date written into software_version.yaml
• Arriba references back to downloading with build_references instead of taking from container
• Arriba visualisation now running with Arriba v2.3.0
• Updated STAR-Fusion to 1.12.0

Fixed

• AWS megatest to display on nf-core website
• arriba visualisation references updated to 2.3.0
• Removed issue with multiple outputs in samtools view for squid

Removed

• FUSIONINSPECTOR_DEV process as the option fusioninspector_limitSjdbInsertNsj is part of the main starfusion release

IMPORTANT Since STAR has been updated, a new STAR index needs to be built as reference. nextflow run nf-core/rnafusion --genomes_base /PATH/TO/REFERENCES --starindex --build_references --outdir OUTDIR -profile singularity or docker

Added

• FusionCatcher single_end support for single reads ABOVE 130 bp
• --fusioninspector_only parameter to run FusionInspector standalone feeding gene list manually with parameter --fusioninspector_fusions PATH
• --fusioncatcher_limitSjdbInsertNsj parameter to feed —limitSjdbInsertNsj to FusionCatcher
• --fusioninspector_limitSjdbInsertNsj parameter to feed —limitSjdbInsertNsj to FusionInspector !!Any other value than default will use the dev version of FusionInspector!!
• OPTIONAL trimming option --trim for hard trimming to 75 bp in case of high read-through. Only fusioncatcher uses trimmed reads as STAR-based fusion detection tools are less sensitive to read-through
• picard metrics, STAR final log, and QualiMap output included in MultiQC report

Changed

• seq_platform and seq_center changed from boolean to string
• seq_platform set to an empty string and seq_center set to an empty string if not existing
• Arriba use ensembl references-built starindex independently of starfusion_build parameter
• ftp to http protocol for STARFUSION_BUILD process Pfam-A.hmm.gz download as ftp causes issues on some servers
• Updated README and usage documentation with more detailed information and metro map
• Arriba use ensembl references-built starindex independently of starfusion_build parameter
• Update of the single-end reads support table in README, added recommendation to use single-end reads only in last resort
• STAR updated to 2.7.10a
• Arriba updated to 2.3.0, references for blacklist and protein domains changed to 2.3.0 from singularity/docker container -> arriba download of references not necessary any more
• multiQC updated to 1.13a
• picard updated to 2.27.4
• dumpsoftwareversions module updated to use multiqc=1.12 containers

Fixed

• FusionInspector does not mix sample reads with fusion lists and meta information from other samples anymore
• Arriba visualisation does not mix sample reads with fusion lists and meta information from other samples anymore
• logging of STAR-fusion and fusionreport version

The usage of the pipeline has been updated. It is recommended to reads the usage.md document.

Added

• Added qualimap/rnaseq v2.2.2d from nf-core modules
• Added UCSC gtfToGenePred v377
• Added picard CollectRnaSeqMetrics v2.26.10
• Added picard MarkDuplicates v2.26.10 from nf-core modules
• Added cat/fastqc from nf-core modules
• Added possibility for manually feeding the results of fusions from different tools to speed-up reruns
• STAR-Fusion references can be downloaded or built but downloaded references are NOT RECOMMENDED as not thoroughly tested (—starfusion_build parameter is true by default, use —starfusion_build false to use downloaded STAR-Fusion references).

Changed

• Upgrade default ensembl version to 102
• Upgrade to nf-core/tools v2.3.2
• Upgrade Arriba v1.2.0 to Arriba v2.2.1
• Upgrade FusionCatcher v1.20 to FusionCatcher v1.33
• Upgrade STAR-fusion v1.8.1 to STAR-fusion v1.10.1
• Upgrade STAR v2.7.1 to STAR v2.7.9
• Upgrade fusion-report v2.1.3 to fusion-report v2.1.5
• Upgrade kallisto v0.44.0 to kallisto v0.46.2
• Upgrade fastqc v0.11.8 to fastqc v0.11.9
• Upgrade samtools v1.9 to samtools v1.15.1
• Upgrade arriba references from v1.2.0 to v2.1.0
• Upgrade fusioncatcher references from v98 to v102
• Use arriba (detect only), kallisto and STAR from nf-core modules
• Instead of separate script to build the references, added —build_references argument in the main —fasta argument is not required with —build_references and set by default to the ensembl references built in the detection workflow

Removed

• Ericscript tool
• GRCh37 support. Subdirectory with params.genome are removed
• Running with conda

[1.2.0] nfcore/rnafusion - 2020/07/15

• Fusion gene detection tools:
  • Arriba v1.2.0
  • Ericscript v0.5.5
  • Fusioncatcher v1.20
  • Pizzly v0.37.3
  • Squid v1.5
  • STAR-Fusion v1.8.1
• Visualization tools:
  • Arriba v1.2.0
  • FusionInspector v2.2.1
• Other tools:
  • fusion-report v2.1.3
  • FastQ v0.11.8
  • MultiQC v1.7
  • STAR aligner v2.7.1a

Added

• Added social preview image #107
• Simplified running the pipeline, better documentation

Changed

• Upgrade fusion-report v2.1.2 to fusion-report v2.1.3
• Upgrade fusion-report v2.1.1 to fusion-report v2.1.2
• Upgrade fusion-report v2.1.0 to fusion-report v2.1.1
• Upgrade Arriba v1.1.0 to Arriba v1.2.0
• Upgrade fusion-report v2.0.2 to fusion-report v2.1.0

Fixed

• Missing strip-components in download-references.nf/star-fusion #148
• Missing version prefix for cdna #143
• samtools missing header in empty file for FusionInspector ref
• Removed profile from helper scripts #139
• Wrong url path for Pfam-A.hmm.gz #140

Removed

• Removed scripts/download-singularity-img.sh and download-singularity-img.nf as they are not necessary any more

v1.1.0 - 2020/02/10

• Fusion gene detection tools:
  • Arriba v1.1.0
  • Ericscript v0.5.5
  • Fusioncatcher v1.20
  • Pizzly v0.37.3
  • Squid v1.5
  • STAR-Fusion v1.6.0
• Visualization tools:
  • Arriba v1.1.0
  • FusionInspector v1.3.1
• Other tools:
  • fusion-report v2.0.1
  • FastQ v0.11.8
  • MultiQC v1.7
  • STAR aligner v2.7.0f

Added

• Added Arriba 1.1.0 #63
• Added Batch mode #54

Changed

• Updated examples and configurations
• Upgraded fusion-report v1.0.0 to fusion-report v2.0.1
• Divided running_tools into fusion and visualization tools
• Updated STAR in Squid, Fusion-Inspector version to 2.7.0f
• Upgraded STAR-Fusion v1.5.0 to STAR-Fusion v1.6.0 #83
• Parameter igenomesIgnore renamed to igenome #81
• Finished STAR-Fusion file renaming #18
• Updated logos
• Updated to nf-core 1.8 TEMPLATE

Fixed

• iGenomes optional, but not really #91
• Updated fusioncatcher to latest 1.20 version also solving #95

Removed

• Variables pizzly_fasta and pizzly_gtf have been removed and replaced with transcript and gtf
• Jenkisfile, test configuration, pylintrc configuration
• Removed igenomes.config because the pipeline only supports Ensembl version

v1.0.2 - 2018/05/16

Changed

• Bumped nf-core template to 1.6 #69

Fixed

• Fixed COSMIC parameters not wrapped in quotes #75
• Implemented output output for fusion tools #72
• Fixed reference download link for STAR-Fusion #71

v1.0.1 - 2018/04/06

Added

• Added support for extra parameters for tools STAR-Fusion, FusionCatcher and fusion-report
• Added example configuration for singularity and docker
• Added fusion-report into the stack #62, #55, #53, #51
• Added nextflow helper script download-singularity-img.nf
• Added nextflow helper script download-references.nf
• Added Jenkinsfile for in-house testing

Changed

• Updated installation of FusionCatcher (available now on bioconda)

Fixed

• Fixed empty symlinks (input.X) in fusion-report #68
• Fixed FASTA issues #60
• Fixed centralized nf-core/config #64
• Fixed scrape_software_versions.py to parse tools versions correctly #65

Removed

• Removed Singularity

Initial release of nf-core/rnafusion 🎉

This is the first production release under nf-core flag previously under SciLifeLab/NGI-RNAfusion.

This version includes:

• Fusion gene detection tools:
  • STAR-Fusion v1.5.0
  • Fusioncatcher v1.00
  • Ericscript v0.5.5
  • Pizzly v0.37.3
  • Squid v1.5
• Visualization tools:
  • FusionInspector v1.3.1
• Other tools:
  • Summary report v1.0
  • FastQ v0.11.8
  • MultiQC v1.7
  • FusionGDB updated at 2019/01/23

Thanks to everyone that contributed to this release 💪 Special thanks go to @MaxUlysse, @alneberg, @ewels, @szilvajuhos and @apeltzer