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