nf-core/rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

alternative-splicingrnarna-seqsplicing

Launch version 2.0.0 https://github.com/nf-core/rnasplice

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nf-core/rnasplice: Changelog

v2.0.0 - Fenix Reborn - [2026-10-20]

The first release since 1.0.4 in April 2024 brings the pipeline up to the nf-core template 4.1.0, Nextflow 26.04 and nf-schema.

Highlights

New LeafCutter (--leafcutter) and IsoformSwitchAnalyzeR (--isoformswitchanalyzer) analyses
Every local module and subworkflow follows the nf-core template and has its own nf-tests, and the pipeline tests cover all four --source values with conda, Docker and Singularity
The AWS iGenomes STAR indices work with a current STAR version

Breaking changes

Detailed in the sections below:

Nextflow 26.04.0 or later is required (#210)
--max_cpus, --max_memory and --max_time are replaced by process.resourceLimits (#163)
--rmats_paired_stats is off by default (#212)
DEXSeq counts BAM input following the samplesheet strandedness (#263)
Some rMATS and SUPPA output paths and file names changed (#285, #309)
The DEXSeq exon and DTU results are named {contrast}.dexseq.*, and the exon tables are TSV instead of CSV (#327)
The DEXSeq log2 fold changes are treatment over control, as the contrast name says, where 1.x reported control over treatment (#327)
The SUPPA dPSI is treatment minus control, where 1.x reported control minus treatment (#328)
The samplesheets of the BAM and Salmon sources need unique sample names (#285)

Added

#161 - Add LeafCutter splicing quantification with --leafcutter, off by default (by @lpantano, @abartlett004)
#163 - Add IsoformSwitchAnalyzeR with --isoformswitchanalyzer (by @lathikaa)
#200 - Add --ignore_tx_version to ignore transcript versions in tximport, for tx2gene files whose transcript IDs carry no version (e.g. from GENCODE) (requested by @Oliverfeudj, done by @piplus2)
#204 - Improve documentation for --rmats_paired_stats (requested by @mlbonatelli, done by @piplus2)
#212 - Add test config for unpaired rMATS (by @piplus2)
#257 - Add a test_dexseq_gff profile and a pipeline level nf-test for a user supplied DEXSeq annotation (--gff_dexseq) (by @piplus2)
#258 - Add pipeline level nf-tests for --source genome_bam, transcriptome_bam and salmon_results, which had no test coverage (by @piplus2)
#261 - Add a pipeline nf-test for samples split over several runs (by @piplus2)
#263 - Accept optional strandedness and single_end columns when starting from --source genome_bam or transcriptome_bam, defaulting to unstranded and paired end (requested by @albamasmalavila, done by @piplus2)
#272 - Add a test_leafcutter profile and a pipeline level nf-test for --leafcutter, which had no test coverage at all (by @piplus2)
#272 - Add the STRAND_JUNCTIONS module, which gives the junctions of an unstranded sample a strand from the splice motif and the annotation (by @piplus2)
#264 - Add an nf-test for the DEXSEQ_DTU module, which had no test coverage (by @piplus2)
#281 - Add an nf-test for the ISOFORMSWITCHANALYZER module, which had no test coverage (by @piplus2)
#281 - Redraw the pipeline metro map with nf-metro, now covering LeafCutter, the --source inputs and the coverage tracks. The .mmd source lives next to the SVG in docs/images/ (by @piplus2)
#285 - Add nf-tests for the RMATS_POST module, which had no test coverage: unpaired, paired, single condition and stub (by @piplus2)
#302 - Add nf-tests for the MISOPY_SASHIMIPLOT module, which had no test coverage of its own (by @piplus2)
#303 - Add nf-tests for the MERGEEVENTS module, which had no test coverage (by @piplus2)
#305 - Add nf-tests for the DEXSEQ_EXON module, which had no test coverage of its own (by @piplus2)
#308 - Add nf-tests for the CLUSTERGROUPS module, which had no test coverage (by @piplus2)
#309 - Add nf-tests for the SUPPA subworkflow: local events and isoforms, local events only, the diffSplice and clustering flags of each level, and stub (by @piplus2)
#310 - Add nf-tests for the TX2GENE_TXIMPORT subworkflow, which had no test coverage of its own: Salmon directories, Salmon tarballs and stub (by @piplus2)
#311 - Add real and stub nf-tests for the MISOPY_SETTINGS module, which had no module test coverage (by @felixhaidle)

Changed

#163 - Breaking change: --max_cpus, --max_memory and --max_time are removed. Cap resources with process.resourceLimits in a config file instead (by @lathikaa)
#163 - Migrate from nf-validation to nf-schema and sync with the nf-core template 3.0.2 (by @lathikaa)
#195 - Sync with the nf-core template 4.0.2, migrate samplesheet and contrastsheet validation from Python scripts to nf-schema, move local modules to TOOL/SUBTOOL/main.nf, track software versions with topic: versions and replace the deprecated CUSTOM_GETCHROMSIZES with SAMTOOLS_FAIDX (by @piplus2)
#195 - PIPELINE_INITIALISATION handles all four input sources (fastq, genome_bam, transcriptome_bam, salmon_results) (by @piplus2)
#207 - Update StageR to 1.32.0, HTSeq to 2.1.2 and DEXSeq to 1.56.0 (by @piplus2)
#210 - Breaking change: Bump nf-schema to 2.7.2 and apply static typing to params in main.nf. The minimum Nextflow version is now 26.04.0 (by @piplus2)
#212 - Breaking change: Default --rmats_paired_stats to false. The paired test requires a specific paired design in the samplesheet, so it is now opt in, see the documentation (by @piplus2)
#215 - Refactor the dexseq modules to the nf-core module template (by @piplus2)
#219 - Rename MISO_INDEX and MISO_RUN to MISOPY_INDEX and MISOPY_RUN and refactor them to the nf-core module template (by @piplus2)
#220 - Remove parse_miso_index.py, which misopy does not need (by @piplus2)
#221 - Refactor SUBREAD_FLATTENGTF to the nf-core module template (by @piplus2)
#225 - DEXSEQ_EXON runs DEXSeq in parallel through BPPARAM, defaulting to SerialParam() (by @piplus2)
#229 - Use the nf-core SUPPA modules and move the SUPPA helper modules to modules/local (by @piplus2)
#238, #244, #253 - Sync with the nf-core templates 4.0.3, 4.1.0 and 4.1.0-2 (by @piplus2)
#242 - Refactor the misopy modules to the nf-core module template (by @piplus2)
#243 - Remove the unused contrast_check workflow (by @piplus2)
#245 - Refactor TXIMPORT to the nf-core module template, update bioconductor-tximeta 1.8.0 -> 1.28.2 (tximport 1.38.2, R 4.0 -> 4.5) and default --ignore_tx_version to FALSE (by @piplus2)
#246 - Replace the local LEAFCUTTER_CLUSTER module and bin/leafcutter_cluster_regtools.py with the nf-core leafcutter/clusterregtools module (by @piplus2)
#247 - Rename GTF_2_GFF3 to GFFREAD_GTF2GFF3 and refactor it to the nf-core module template (by @piplus2)
#248 - Move GFFREAD_TX2GENE to modules/local/gffread/tx2gene and update gffread 0.12.1 -> 0.12.7 (by @piplus2)
#249 - Refactor STAGER to the nf-core module template and expose the stageR options through ext.args (--alpha, --method, --allow_na, --only_significant_genes, --order), which were previously ignored. Defaults are unchanged (by @piplus2)
#250 - Move the VISUALISE_MISO subworkflow to the nf-core subworkflow template (by @piplus2)
#251 - Rename DRIMSEQ_FILTER to DRIMSEQ_DMFILTER and refactor it to the nf-core module template (by @piplus2)
#254 - Rename GTF_GENE_FILTER to GTFGENEFILTER and refactor it to the nf-core module template. bin/filter_gtf_for_genes_in_genome.py is now a module template (by @piplus2)
#255 - Refactor EDGER_EXON to the nf-core module template. bin/run_edger_exon.R is now a module template, --n_edger_plot moves to ext.args and the inputs and outputs carry a meta map (by @piplus2)
#256 - Move the ALIGN_STAR subworkflow to the nf-core subworkflow template, with nf-tests for both the STAR_ALIGN and the STAR_ALIGN_IGENOMES paths (by @piplus2)
#257 - Move the DEXSEQ_DEU subworkflow to the nf-core subworkflow template (by @piplus2)
#257 - DEXSEQ_DEU emits the DEXSeq exon count tables sorted by file name, and takes an explicit skip_annotation input instead of reading params.gff_dexseq (by @piplus2)
#261 - The pipeline parses the samplesheet and the contrastsheet once each, in PIPELINE_INITIALISATION (by @piplus2)
#261 - Remove the unused INPUT_CHECK subworkflow (by @piplus2)
#264 - Move the DRIMSEQ_DEXSEQ_DTU subworkflow to the nf-core subworkflow template (by @piplus2)
#268 - Move the EDGER_DEU subworkflow to the nf-core subworkflow template. It now emits the EDGER_EXON results and the featureCounts tables, which it ran but discarded (by @piplus2)
#270 - Move the LEAFCUTTER subworkflow to the nf-core subworkflow template. Its juncs output is now the per sample [ meta, junc ] tuples, instead of a single list flattening the meta maps in with the paths (by @piplus2)
#272 - --leafcutter now works with --source genome_bam, whatever the strandedness, since the junction strand no longer has to come from the alignment. For unstranded libraries the clusters differ slightly from LeafCutter’s documented STAR route, see the LeafCutter section of docs/usage.md (by @piplus2)
#281 - Refactor ISOFORMSWITCHANALYZER to the nf-core module template and update IsoformSwitchAnalyzeR 2.2.0 -> 2.12.0 (R 4.3 -> 4.5). bin/run_isoformswitchanalyzer.R is now a module template (by @piplus2)
#284 - Refactor PREPROCESS_TRANSCRIPTS_FASTA_GENCODE to the nf-core module template, with environment.yml, meta.yml, a stub and nf-tests. It reports the coreutils version of cut, which does the work, instead of sed (by @piplus2)
#285 - Replace the local RMATS_PREP module with the nf-core rmats/prep module, which preps each BAM file once and on its own instead of every BAM file of a contrast in one go, and refactor RMATS_POST to the nf-core module template, with environment.yml, meta.yml, a stub and the --paired-stats, --cstat and --novelSS options in ext.args. It also reports the PAIRADISE version (by @piplus2)
#285 - Breaking change: The rMATS .rmats files are published to rmats/prep/{sample}.rmats and the results of a contrast to rmats/{contrast}{_paired}/, with the log next to the folder. The intermediate tmp/ folder of the post step is no longer published (by @piplus2)
#285 - Breaking change: The samplesheet of --source genome_bam, transcriptome_bam and salmon_results must have unique sample names, which the schema now checks up front. Duplicates already collided in the per sample outputs, since only the fastq source merges the runs of a sample (by @piplus2)
#286 - Replace the local STAR_ALIGN_IGENOMES module with the nf-core star/align module, aliased and pinned in conf/modules.config to the STAR 2.6.1d container that reads the AWS iGenomes indices. The --seq_center read group tag is set in ext.args and now applies to every STAR alignment, not only to the iGenomes path (by @piplus2)
#287 - Replace the local STAR_GENOMEGENERATE_IGENOMES module with the nf-core star/genomegenerate module, aliased and pinned in conf/modules.config to the same STAR 2.6.1d container as STAR_ALIGN_IGENOMES (by @piplus2)
#289 - Drop the STAR 2.6.1d pin. A supplied STAR index now goes through the new STAR_GENOMEPARAMS_UPGRADE module, which rewrites the genomeParameters.txt metadata that STAR 2.7.4a and later validate and copies the binary index files through untouched, so the AWS iGenomes indices work with a single STAR version. This removes the STAR_ALIGN_IGENOMES and STAR_GENOMEGENERATE_IGENOMES aliases, the legacy --quantTranscriptomeBan argument and the is_aws_igenome flag (suggested by @pinin4fjords, done by @piplus2)
#290 - Move the PREPARE_GENOME subworkflow to the nf-core subworkflow template. It takes --source, --aligner, --pseudo_aligner and --skip_alignment as inputs instead of reading params, and the GTF converted from --gff is named after the GFF file instead of null.gtf (by @piplus2)
#291 - Move the RMATS subworkflow to the nf-core subworkflow template. It takes the genome BAM files as [ meta, bam ] and reads the condition from the meta map, and it also emits the bam lists. The BAM files of a contrast are listed in samplesheet order in both the paired and the unpaired model (by @piplus2)
#301 - Refactor SPLIT_FILES to the nf-core module template, with nf-tests. The split SUPPA files keep the values as SUPPA wrote them, so missing PSI values stay nan instead of becoming NA (by @piplus2)
#306 - Refactor CREATE_BAMLIST to the nf-core module template, with nf-tests, a stub and a Seqera container (by @piplus2)
#308 - Refactor CLUSTERGROUPS to the nf-core module template. The contrast conditions travel in the meta map, the versions are reported through a topic eval tuple and the container holds Python only (by @piplus2)
#309 - Move the SUPPA subworkflow to the nf-core subworkflow template. The local event and isoform analyses share a single SPLIT_FILES_PSI, SUPPA_DIFFSPLICE, CLUSTERGROUPS and SUPPA_CLUSTEREVENTS call, with the level in the meta map, and CLUSTERGROUPS gives the column ranges to SUPPA_CLUSTEREVENTS as a value instead of a file read in the subworkflow (by @piplus2)
#309 - Breaking change: Move the merged SUPPA local events from a top level mergeevents/ folder to suppa/generate_events/per_local_event/merged_events/ (by @piplus2)
#309 - Breaking change: Rename the SUPPA cluster group files after their level, so GBR-YRI_groups.txt becomes local_GBR-YRI_groups.txt, with a new transcript_GBR-YRI_groups.txt next to it (by @piplus2)
#310 - Move the TX2GENE_TXIMPORT subworkflow to the nf-core subworkflow template. It detects a tarball from the file name instead of the first element of the path, and no longer adds a tgz key to the meta map of the Salmon results it emits (by @piplus2)
#311 - Correct MISOPY_SETTINGS metadata and remove redundant prefix argument parsing and configuration overrides (by @felixhaidle)
#327 - Rename the local modules CREATE_BAMLIST, STRAND_JUNCTIONS, SPLIT_FILES and STAR_GENOMEPARAMS_UPGRADE to CREATEBAMLIST, STRANDJUNCTIONS, SPLITFILES and GENOMEPARAMSUPGRADE, and move RMATS_POST to modules/local/rmats/post. Custom configs that select these processes with withName need the new names (suggested by @mashehu, done by @piplus2)
#327 - Replace the local DEXSeq modules with the nf-core modules dexseq/prepareannotation, dexseq/count, dexseq/exon and dexseq/dtu. The DEXSeq annotation is prepared with a fixed Python hash seed, so it is the same across runs (suggested by @mashehu, done by @piplus2)
#327 - Breaking change: DEXSEQ_EXON and DEXSEQ_DTU run once per contrast, and their results are named {contrast}.dexseq.{dataset,results,gene_qvalues}.{rds,tsv} and {contrast}.dexseq.plots.pdf, so the exon tables are TSV instead of CSV. The log2 fold changes are now treatment over control, where the local scripts reported control over treatment (reported by @erikrikarddaniel, fix by @piplus2)
#327 - DEXSEQ_DEU takes skip_annotation instead of prepare_annotation, and Salmon gets empty inputs instead of the assets/dummy_file*.txt placeholders (suggested by @mashehu, done by @piplus2)
#327 - Add icons, bounds and tidier descriptions to the parameter schema, the LeafCutter and RegTools citations, and fix the profile names in the conf/test_*.config headers (suggested by @mashehu and @erikrikarddaniel, done by @piplus2)

Fixed

#195 - Fix Nextflow 26+ compatibility: no deprecated if/else blocks in nextflow.config, ext.when closures in conf/modules.config and no switch/case statements (by @piplus2)
#195 - Fix channel reuse in the SUPPA subworkflow, CREATE_BAMLIST null paths for single condition rMATS runs, SUBREAD_FLATTENGTF multi-line versions breaking the YAML and the STAR_ALIGN argument renamed to --quantTranscriptomeSAMoutput (by @piplus2)
#198 - Do not pass sorted BAM files to Salmon (reported by @albamasmalavila, fix by @piplus2)
#199 - Fix the ignored --clip_r1 and --clip_r2 arguments of TRIMGALORE (reported by @misiti-1864309, fix by @piplus2)
#201 - Pass the contrasts channel, instead of the samplesheet channel, to RMATS and SUPPA (by @piplus2)
#208 - Follow the nf-core standard for conditional output in publishDir.saveAs (by @piplus2)
#140 - Add validation of sample names for R compatibility (by @fhausmann)
#212 - Fix the sample order of the RMATS paired model, which was not taken from the samplesheet (by @piplus2)
#214 - Fix the missing BPPARAM argument of DEXSEQ_DTU and remove its unused ntop argument (by @piplus2)
#218 - Fix a regex error in parse_miso_index.py (by @piplus2)
#219 - Fix MISOPY handling of paired-end reads and the BAM files passed to it (by @piplus2)
#224 - Fix the sample IDs in the DEXSEQ_DTU script (reported by @albamasmalavila, fix by @piplus2)
#232 - Fix the wrong branch taken when the input is BAM (reported by @albamasmalavila, fix by @piplus2)
#238 - Add a missing backslash in the mergeevents command (by @piplus2)
#241 - Add a missing backslash in the clustergroups command (by @piplus2)
#245 - Fix the ignored --tximport_ignore_tx_version argument of TXIMPORT (by @piplus2)
#254 - Fix GTFGENEFILTER logging the characters of the last GTF sequence name instead of the sequence names found, and raising a NameError on an empty GTF. It now fails explicitly when no GTF feature matches the genome FASTA (by @piplus2)
#255 - Fix EDGER_EXON writing an unreadable zero-page PDF when a contrast has no gene to plot. It now fails explicitly on missing samplesheet or contrastsheet columns, on a sample assigned to more than one condition, on a contrast condition absent from the samplesheet and on a missing featureCounts table (by @piplus2)
#256 - Fix the software version commands of STAR_ALIGN_IGENOMES and STAR_GENOMEGENERATE_IGENOMES, which failed with a shell syntax error and aborted both processes (by @piplus2)
#256 - Use --quantTranscriptomeBan Singleend on the iGenomes path, as the pinned STAR 2.6.1d does not accept --quantTranscriptomeSAMoutput (by @piplus2)
#257 - Fix --gff_dexseq aborting with Not a valid argument for 'combine' operator [String]. RNASPLICE overwrote the ch_dexseq_gff channel it receives from PREPARE_GENOME with the raw parameter string (by @piplus2)
#258 - Fix --source genome_bam, transcriptome_bam and salmon_results aborting at startup, as the samplesheet was always validated against the fastq schema. The schema is now selected from --source by samplesheetSchema() (by @piplus2)
#258 - PIPELINE_INITIALISATION parses the samplesheet and passes it through NFCORE_RNASPLICE into RNASPLICE, as in the nf-core template. RMATS receives that samplesheet channel instead of a second file(params.input), and the rMATS single condition check goes through the same source schema instead of reading the CSV with new File/new URL, which only handled local and http paths (by @piplus2)
#258 - Fix BAM_SORT_STATS_SAMTOOLS being called with a bare fasta path in the genome_bam and transcriptome_bam paths, which aborted the run (by @piplus2)
#258 - Fix No such variable: ch_txi_suppa_tpm with --source salmon_results and --suppa (by @piplus2)
#258 - Fix ISOFORMSWITCHANALYZER receiving the .tar.gz archives instead of the extracted Salmon directories with --source salmon_results. TX2GENE_TXIMPORT extracts them and now emits them (by @piplus2)
#261 - Fix the paired rMATS sample order when a sample spans several samplesheet rows (by @piplus2)
#261 - Fix single condition rMATS runs, which aborted before producing any output (by @piplus2)
#284 - Fix --gencode with --transcript_fasta aborting in PREPARE_GENOME, as PREPROCESS_TRANSCRIPTS_FASTA_GENCODE dropped the meta map the downstream channel expects (by @piplus2)
#261 - Fix samples split over several samplesheet rows, whose fastq files were passed on without being concatenated (by @piplus2)
#263 - Breaking change: DEXSEQ_COUNT no longer counts BAM input as forward stranded, it follows the samplesheet strandedness, so DEXSeq results change for BAM samplesheets that do not set the column (reported by @albamasmalavila, fix by @piplus2)
#264 - Fix the DEXSEQ_DTU stub, which wrote file names the process outputs did not match, so a stub run of the DTU path failed (by @piplus2)
#266 - Fix DEXSEQ_DTU, which ignored task.cpus and ran DEXSeq on every core of the host, as parallel::detectCores() does not see the container cpu limit. It now takes the worker count from task.cpus and defaults to SerialParam(), as DEXSEQ_EXON has since #225 (by @piplus2)
#267 - Fix SPLIT_FILES, whose stub wrote an unescaped $ that Nextflow 26.08-edge refuses to parse, taking the whole pipeline down with it as SUPPA could no longer import the module (by @piplus2)
#271 - Fix --leafcutter, which aborted at REGTOOLS_JUNCTIONSEXTRACT with invalid option -- 'i'. The intron length arguments were the -i/-I of regtools 0.5.x, which 1.0.0 spells -m/-M (by @piplus2)
#272 - Fix --leafcutter clustering nothing. regtools now takes the junction strand from the samplesheet strandedness, and the junctions of an unstranded sample are stranded afterwards from the splice motif and the annotation, so the BAM files the other analyses read are left alone (by @piplus2)
#275 - Fix missing yaml from singularity container in GTFGENEFILTER (reported by @srira25, fix by @piplus2)
#277 - Fix missing pyyaml from singularity container in STRAND_JUNCTIONS, CLUSTERGROUPS and MISOPY_SETTINGS (by @piplus2)
#281 - Fix ISOFORMSWITCHANALYZER writing common_switch_consequences.pdf next to the results directory instead of inside it, so it was never published (by @piplus2)
#290 - Fix an uncompressed --salmon_index or --suppa_tpm, which reached SALMON_QUANT and SUPPA still wrapped with an empty meta map (by @piplus2)
#291 - Fix --rmats_paired_stats with conditions of different sizes, which dropped the samples with no counterpart without a warning instead of stopping with an error. A contrast naming a condition with no sample now also stops with an error instead of being skipped (by @piplus2)
#303 - Fix MERGEEVENTS hanging when the last SUPPA event file holds no events, only its header (by @piplus2)
#304 - Fix the pipeline stopping at launch with Nextflow 26.09 edge releases, which take a parameter without a default as required unless it is declared nullable. The optional parameters are now nullable (by @piplus2)
#305 - Fix the stub of DEXSEQ_EXON, whose output files now take their names from the contrastsheet like those of the script (by @piplus2)
#309 - Publish the SUPPA cluster groups with --source salmon_results, and publish the groups of both levels instead of one overwriting the other (by @piplus2)
#312 - Remove the 4 cpu, 12 GB and 12 h caps from the test_full profile, which are too small for STAR to align to GRCh37 in the AWS full size test (by @piplus2)
#315 - Fix the AWS tests stopping at launch on the Seqera Platform, which ran an older Nextflow with the old syntax parser (by @piplus2)
#316 - Fix the AWS full size test failing at paramsSummaryLog, as its Slack config dropped the pinned nf-schema version (by @piplus2)
#317 - Restore the MultiQC screenshots of the output docs, which the template update to nf-core/tools 3.0.0 deleted (by @piplus2)
#320 - Fix SUPPA with -profile conda, where a newer statsmodels lacked the multipletests import of SUPPA 2.4. The SUPPA modules now pin statsmodels 0.14.6, as in their container (by @piplus2)
#321 - Fix local modules giving different results with -profile conda and the containers: pin R and its packages to the container versions for DRIMSeq, edgeR and tximport, compare the edgeR result tables rounded to 6 significant digits in the tests, and stop the GFF3 header of GFFREAD_GTF2GFF3 from being padded with tabs in the container (by @piplus2)
#323 - Fix the pipeline tests with -profile conda and Nextflow 26.09: the sorted BAM files, whose headers differ between the conda and container builds of samtools, are snapshotted by their alignments with nft-bam, and the rMATS test of unequal paired sample counts also looks for the error in stderr, where Nextflow 26.09 prints it (by @piplus2)
#324 - Update the nf-core SUPPA modules, which now pin statsmodels and report its version, replacing the patches of #320 (by @piplus2)
#325 - Redraw the metro map with nf-metro 2.1.0, with larger stations, labels and spacing so the single-line stations are easier to read, and the transcript quantification under the exon and junction based analysis (suggested by @mashehu, done by @piplus2)
#327 - Default --ignore_tx_version to false, as documented, and fix TXIMPORT stopping with versioned transcript IDs when it is true: the transcript tables now drop the versions too (reported by @erikrikarddaniel, fix by @piplus2)
#327 - Accept decimal values for --diffsplice_lower_bound, --diffsplice_tpm_threshold and --diffsplice_nan_threshold, which SUPPA reads as decimals but the schema typed as integers (by @piplus2)
#327 - Declare --rmats_paired_stats without a true default in main.nf, which contradicted the documented false that nextflow.config sets (reported by @erikrikarddaniel, fix by @piplus2)
#328 - Breaking change: SUPPA and IsoformSwitchAnalyzeR report treatment minus control, like the other tools, where they reported control minus treatment. The SUPPA dPSI columns are named {level}_{control}-{level}_{treatment}_dPSI, where {level} is local or transcript, and the .psivec columns list the control samples first. The IsoformSwitchAnalyzeR plot folders are named {control}_vs_{treatment}. Each tool names a comparison after its first and second condition (suggested by @erikrikarddaniel, done by @piplus2)
#329 - Fix the devcontainer setup script, which lacked the executable bit, so the devcontainer did not start in VS Code on macOS (by @tfallon-ionis)