Sample agat arriba filter_arriba_main.py pandas pyyaml python contamination_skipped_low_reads ctat-splicing fastp fastqc STAR-Fusion fusion_report fusion_report DB retrieval gatk4 samtools perl kallisto expression_qc_and_signatures picard preseq preseq_to_multiqc rseqc rseqc_to_multiqc seqtool_to_multiqc filter_starfusion_main.py numpy boto3 star gawk HGNC DB retrieval nf-core/rnafusion Nextflow
AGAT_CONVERTSPGFF2TSV 1.2.0
ARRIBA 2.4.0
ARRIBA_FILTER 1.0 3.0.0 6.0.3
ARRIBA_VISUALISATION 2.4.0
CANCER_INTRONS_TO_VCF 3.11.0
CONTAMINATION_SKIPPED_LOW_READS 1.0.0
CTATSPLICING_STARTOCANCERINTRONS 0.0.3
FASTQC 0.12.1
FASTQC_FOR_FASTP 0.12.1
FUSIONINSPECTOR 1.12.0
FUSIONREPORT 2.1.5 null
GATK4_MARKDUPLICATES 4.4.0.0 1.17
GTF2BED 5.26.2
KALLISTO_QUANT 0.51.1
KALLISTO_TO_TX2GENE_QC 3.11.0 1.0.0
PICARD_COLLECTINSERTSIZEMETRICS 3.1.0
PICARD_COLLECTRNASEQMETRICS null
PRESEQ_LCEXTRAP 3.2.0
PRESEQ_TO_MULTIQC 3.11.14 1.0.0
RSEQC_BAMSTAT 5.0.2
RSEQC_INFEREXPERIMENT 5.0.2
RSEQC_INNERDISTANCE 5.0.2
RSEQC_JUNCTIONANNOTATION 5.0.2
RSEQC_JUNCTIONSATURATION 5.0.2
RSEQC_READDISTRIBUTION 5.0.2
RSEQC_READDUPLICATION 5.0.2
RSEQC_TO_MULTIQC 3.11.14 1.0.0
SAMTOOLS_INDEX_ALIGNMENT_CRAM 1.17
SAMTOOLS_INDEX_STAR_ALIGNMENT 1.17
SAMTOOLS_VIEW_ALIGNMENT_CRAM 1.17
SEQTOOL_TO_MULTIQC 3.11.14 1.0.0
STARFUSION 1.12.0
STARFUSION_FILTER 3.0.0 6.0.3 1.0 2.4.1 unknown
STAR_ALIGNMENT 1.16.1 2.7.10a0 5.1.0
VCF_COLLECT 3.11.0 2025-01-22/23:32
Workflow v3.0.2-g1149ea1 25.10.2
fastp 0.23.4