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nf-core/rnafusion: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v3.0.1 - [2023-11-29]

Added

Changed

  • python3 explicit in vcf_collect #452

Fixed

  • software-version.yml and in general version track-keeping was incomplete #451

Removed

v3.0.0 - [2023-11-27]

Added

  • Add picard CollectInsertSizeMetrics to QC workflow #408
  • Build CRAM index in the same directory as CRAM files for Arriba and STAR-Fusion #427

Changed

  • Replace PICARD_MARKDUPLICATES with GATK4_MARKDUPLICATES #409
  • Removed --fusioninspector_filter and --fusionreport_filter in favor of --tools_cutoff (default = 1, no filters applied) #389
  • Now publishing convert2bed output to convert2bed to keep the output file #420
  • No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) #420
  • --annotate --examine_coding_effect to collect more data from fusioninspector #426
  • Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report #443
  • Arriba updated to 2.4.0 #429
  • Change megafusion into vcf_collect, taking into account e.g. the annotation and coding effects outputs from fusioninspector, HGNC ids, frame status... #414
  • CI tests on --all instead of each tool separately, and include trimmed/not trimmed matrix tests #430
  • AWS tests on --all instead of each tool separately, and include trimmed/not trimmed matrix tests #433
  • Update fusion-report to 2.1.8, updated COSMIC database to fix 404 error, fix download of references via proxy and removing FusionGDB database #445
  • Update documentation #446

Fixed

  • Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests #416
  • Update modules, and make sure MultiQC displays the QC results properly #440
  • Add 'when' condition to run CollectInsertSizeMetrics only when STAR-fusion bam files are available #444

Removed

  • Remove squid and pizzly fusion detection tools #406
  • Remove harsh trimming option --trim #413
  • Remove qualimap rna_seq #407

v2.4.0 - [2023/09/22]

Added

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
    • Update metro map #428

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

v2.3.0 - [2023/04/24]

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

Removed

v2.2.0 - [2023/03/13]

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

v2.1.0 - [2022/07/12]

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

Removed

v2.0.0 - [2022/05/19]

Update to DSL2 and newer software/reference versions

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
  • CI test done on stubs of reference building for subprocesses ensembl and arriba

Parameters for STAR for arriba changed from:

--readFilesCommand zcat \\
        --outSAMtype BAM Unsorted \\
--outStd BAM_Unsorted \\
--outSAMunmapped Within \\
--outBAMcompression 0 \\
--outFilterMultimapNmax 1 \\
--outFilterMismatchNmax 3 \\
--chimSegmentMin 10 \\
--chimOutType WithinBAM SoftClip \\
--chimJunctionOverhangMin 10 \\
--chimScoreMin 1 \\
--chimScoreDropMax 30 \\
--chimScoreJunctionNonGTAG 0 \\
--chimScoreSeparation 1 \\
--alignSJstitchMismatchNmax 5 -1 5 5 \\
--chimSegmentReadGapMax 3 \\
--sjdbOverhang ${params.read_length - 1}

to

--readFilesCommand zcat \
--outSAMtype BAM Unsorted \
--outSAMunmapped Within \
--outBAMcompression 0 \
--outFilterMultimapNmax 50 \
--peOverlapNbasesMin 10 \
--alignSplicedMateMapLminOverLmate 0.5 \
--alignSJstitchMismatchNmax 5 -1 5 5 \
--chimSegmentMin 10 \
--chimOutType WithinBAM HardClip \
--chimJunctionOverhangMin 10 \
--chimScoreDropMax 30 \
--chimScoreJunctionNonGTAG 0 \
--chimScoreSeparation 1 \
--chimSegmentReadGapMax 3 \
--chimMultimapNmax 50

As recommended here.

Parameters for STAR for STAR-fusion changed from:

--twopassMode Basic \\
--outReadsUnmapped None \\
--chimSegmentMin 12 \\
--chimJunctionOverhangMin 12 \\
--alignSJDBoverhangMin 10 \\
--alignMatesGapMax 100000 \\
--alignIntronMax 100000 \\
--chimSegmentReadGapMax 3 \\
--alignSJstitchMismatchNmax 5 -1 5 5 \\
--runThreadN ${task.cpus} \\
--outSAMstrandField intronMotif ${avail_mem} \\
--outSAMunmapped Within \\
--outSAMtype BAM Unsorted \\
--outSAMattrRGline ID:GRPundef \\
--chimMultimapScoreRange 10 \\
--chimMultimapNmax 10 \\
--chimNonchimScoreDropMin 10 \\
--peOverlapNbasesMin 12 \\
--peOverlapMMp 0.1 \\
--readFilesCommand zcat \\
--sjdbOverhang ${params.read_length - 1} \\
--chimOutJunctionFormat 1

to

--outReadsUnmapped None \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--outSAMstrandField intronMotif \
--outSAMunmapped Within \
--chimSegmentMin 12 \
--chimJunctionOverhangMin 8 \
--chimOutJunctionFormat 1 \
--alignSJDBoverhangMin 10 \
--alignMatesGapMax 100000 \
--alignIntronMax 100000 \
--alignSJstitchMismatchNmax 5 -1 5 5 \
--chimMultimapScoreRange 3 \
--chimScoreJunctionNonGTAG -4 \
--chimMultimapNmax 20 \
--chimNonchimScoreDropMin 10 \
--peOverlapNbasesMin 12 \
--peOverlapMMp 0.1 \
--alignInsertionFlush Right \
--alignSplicedMateMapLminOverLmate 0 \
--alignSplicedMateMapLmin 30 \
--chimOutType Junctions

Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz used for squid and arriba, Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz used for STAR-fusion and the quality control as the quality control is based on the STAR-fusion alignment.

Fixed

Removed

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

v1.3.0 - [2020/07/15]

  • Using official STAR-Fusion container #160

Added

  • Added social preview image #107
  • Added support for GRCh37 genome assembly #77

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 - [2019/05/13]

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 - [2019/04/06]

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

v1.0 - [2018/02/14]

Version 1.0 marks the first production release of this pipeline under the nf-core flag. The pipeline includes additional help scripts to download references for fusion tools and Singularity images.

Initial release of nf-core/rnafusion, created with the nf-core template.

Added

Fixed

Dependencies

Deprecated