3.0.2

Bug fixes.

Changelog:

Changed

• Update to nf-tools 2.11.1 [https://github.com//pull/457] (#457)
• Update picard collectrnaseqmetrics memory requirements to 0.8x what is provided #474

Fixed

• fix bug when using parameter "whitelist" #466
• fix VCF_COLLECT handling when a tool is absent from FUSIONREPORT report #458
• fix VCF_COLLECT when fusioninspector output is empty but fusionreport is not #465
• fix VCF_COLLECT bug #481
• fix conda package for starfusion/detecthttps://github.com//pull/482
• fix logical gate so when stringtie should run but not starfusion, starfusion will not runhttps://github.com//pull/482

3.0.1

Patch to fix software versions output

3.0.0

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

2.4.0

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

2.3.4

Fix for megafusion

2.3.3

Fix for megafusion (again)

2.3.2

Fixes for megafusion

2.3.1

Changed permissions on megafusion script

2.3.0

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

2.2.0

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