Processes


NFCORE_RNAFUSION:GENERATE_SAMPLE_TYPE_MAP	1
DEMULTIPLEX:BCLCONVERT	8	8
DEMULTIPLEX:FLOWCELL_QC	1
DEMULTIPLEX:AGGREGATE_DEMUX_STATS	1
DEMULTIPLEX:CAT_FASTQ	96	96
DEMULTIPLEX:SAMPLESHEET_FROM_MERGED	1
RNAFUSION:FASTQC	96	96
TRIM_WORKFLOW:FASTP	96	96
TRIM_WORKFLOW:FASTQC_FOR_FASTP	96	96
RNAFUSION:KALLISTO_INDEX	1	1
RNAFUSION:KALLISTO_QUANT	96	96
RNAFUSION:KALLISTO_TO_TX2GENE_QC	96
RNAFUSION:KALLISTO_TO_MULTIQC	96
RNAFUSION:GTF2BED	1
FASTQ_ALIGN_STAR:STAR_ALIGNMENT	96	96
FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT	96	96
RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM	96	96
RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM	96	96
ARRIBA_WORKFLOW:ARRIBA	96		1
ARRIBA_WORKFLOW:ARRIBA_FILTER	96
STARFUSION_WORKFLOW:STARFUSION	96	81	2
STARFUSION_WORKFLOW:STARFUSION_FILTER	96
FUSIONREPORT_WORKFLOW:FUSIONREPORT	96
FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR	94
FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV	94
FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT	94
FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION	94
RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS	96	27	68
RNAFUSION:CANCER_INTRONS_TO_VCF	96
QC_WORKFLOW:GATK4_MARKDUPLICATES	96	84	2
QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS	96	9	51
QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS	96	96
BAM_RSEQC:RSEQC_BAMSTAT	96	96
BAM_RSEQC:RSEQC_INNERDISTANCE	96
BAM_RSEQC:RSEQC_INFEREXPERIMENT	96
BAM_RSEQC:RSEQC_JUNCTIONANNOTATION	96		1
BAM_RSEQC:RSEQC_JUNCTIONSATURATION	96
BAM_RSEQC:RSEQC_READDISTRIBUTION	96		3
BAM_RSEQC:RSEQC_READDUPLICATION	96	92
QC_WORKFLOW:SEQTOOL_QC	96	55	1
QC_WORKFLOW:SEQTOOL_WHOLE_BAM_SATURATION	96	80
QC_WORKFLOW:SEQTOOL_TO_MULTIQC	96
QC_WORKFLOW:PRESEQ_LCEXTRAP	96	47	18
QC_WORKFLOW:PRESEQ_TO_MULTIQC	96
RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE	95	95
RNA_CONTAMINATION_DETECTION_WORKFLOW:EXTRACT_VAF_FEATURES	95
RNA_CONTAMINATION_DETECTION_WORKFLOW:PREDICT_CONTAMINATION	95
RNAFUSION:CONTAMINATION_SKIPPED_LOW_READS	1	1
RNAFUSION:CONTAMINATION_TO_MULTIQC	95
RNAFUSION:MULTIQC	1
RNAFUSION:MULTIQC_GENERAL_STATS_TXT_TO_JSON	1
RNAFUSION:MULTIQC_GENERAL_STATS_TXT_TO_TSV	1
RNAFUSION:MULTIQC_EXTRACT_CONTROLS	1
RNAFUSION:RUN_LEVEL_INTERMEDIATE	1
RNAFUSION:RUN_LEVEL_METRICS	1