Processes


NFCORE_RNAFUSION:GENERATE_SAMPLE_TYPE_MAP	1
DEMULTIPLEX:BCLCONVERT	4	4
DEMULTIPLEX:FLOWCELL_QC
DEMULTIPLEX:AGGREGATE_DEMUX_STATS
DEMULTIPLEX:SAMPLESHEET_CHECK
DEMULTIPLEX:CAT_FASTQ
DEMULTIPLEX:SAMPLESHEET_FROM_MERGED
RNAFUSION:FASTQC
TRIM_WORKFLOW:FASTP
TRIM_WORKFLOW:FASTQC_FOR_FASTP
RNAFUSION:KALLISTO_INDEX	1
RNAFUSION:KALLISTO_QUANT
RNAFUSION:KALLISTO_TO_TX2GENE_QC
RNAFUSION:KALLISTO_TO_MULTIQC
RNAFUSION:GTF2BED	1
FASTQ_ALIGN_STAR:STAR_ALIGNMENT
FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT
RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM
RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM
ARRIBA_WORKFLOW:ARRIBA
ARRIBA_WORKFLOW:ARRIBA_FILTER
STARFUSION_WORKFLOW:STARFUSION
STARFUSION_WORKFLOW:STARFUSION_FILTER
FUSIONREPORT_WORKFLOW:FUSIONREPORT
FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR
FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV
FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT
FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION
RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS
RNAFUSION:CANCER_INTRONS_TO_VCF
QC_WORKFLOW:GATK4_MARKDUPLICATES
QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS
QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS
BAM_RSEQC:RSEQC_BAMSTAT
BAM_RSEQC:RSEQC_INNERDISTANCE
BAM_RSEQC:RSEQC_INFEREXPERIMENT
BAM_RSEQC:RSEQC_JUNCTIONANNOTATION
BAM_RSEQC:RSEQC_JUNCTIONSATURATION
BAM_RSEQC:RSEQC_READDISTRIBUTION
BAM_RSEQC:RSEQC_READDUPLICATION
QC_WORKFLOW:SEQTOOL_QC
QC_WORKFLOW:SEQTOOL_WHOLE_BAM_SATURATION
QC_WORKFLOW:RSEQC_TO_MULTIQC
QC_WORKFLOW:SEQTOOL_TO_MULTIQC
QC_WORKFLOW:PRESEQ_LCEXTRAP
QC_WORKFLOW:PRESEQ_TO_MULTIQC
RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE
RNA_CONTAMINATION_DETECTION_WORKFLOW:EXTRACT_VAF_FEATURES
RNA_CONTAMINATION_DETECTION_WORKFLOW:PREDICT_CONTAMINATION
RNAFUSION:CONTAMINATION_SKIPPED_LOW_READS
RNAFUSION:CONTAMINATION_TO_MULTIQC
RNAFUSION:MULTIQC
RNAFUSION:MULTIQC_GENERAL_STATS_TXT_TO_JSON
RNAFUSION:MULTIQC_GENERAL_STATS_TXT_TO_TSV
RNAFUSION:MULTIQC_EXTRACT_CONTROLS
RNAFUSION:RUN_LEVEL_INTERMEDIATE
RNAFUSION:RUN_LEVEL_METRICS