nf-core/rnafusion: 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 releas