Processes

NFCORE_RNAFUSION:GENERATE_SAMPLE_TYPE_MAP
1
DEMULTIPLEX:BCLCONVERT
8
DEMULTIPLEX:FLOWCELL_QC
1
DEMULTIPLEX:AGGREGATE_DEMUX_STATS
1
DEMULTIPLEX:CAT_FASTQ
96 1
DEMULTIPLEX:SAMPLESHEET_FROM_MERGED
1
RNAFUSION:FASTQC
46 50 8
TRIM_WORKFLOW:FASTP
71 1 24 28
TRIM_WORKFLOW:FASTQC_FOR_FASTP
45 26
RNAFUSION:KALLISTO_INDEX
1
RNAFUSION:KALLISTO_QUANT
44 27
RNAFUSION:KALLISTO_TO_TX2GENE_QC
43 1
RNAFUSION:KALLISTO_TO_MULTIQC
42
RNAFUSION:GTF2BED
1
FASTQ_ALIGN_STAR:STAR_ALIGNMENT
36 35
FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT
31 5
RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM
29 2
RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM
29
ARRIBA_WORKFLOW:ARRIBA
29 7
ARRIBA_WORKFLOW:ARRIBA_FILTER
28
STARFUSION_WORKFLOW:STARFUSION
14 20 18
STARFUSION_WORKFLOW:STARFUSION_FILTER
12 1
FUSIONREPORT_WORKFLOW:FUSIONREPORT
12
FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR
FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV
FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT
FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION
RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS
29 2
RNAFUSION:CANCER_INTRONS_TO_VCF
29
QC_WORKFLOW:GATK4_MARKDUPLICATES
26 10
QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS
19 12
QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS
29 7
BAM_RSEQC:RSEQC_BAMSTAT
26 5
BAM_RSEQC:RSEQC_INNERDISTANCE
30 1
BAM_RSEQC:RSEQC_INFEREXPERIMENT
31
BAM_RSEQC:RSEQC_JUNCTIONANNOTATION
27 4
BAM_RSEQC:RSEQC_JUNCTIONSATURATION
28 3
BAM_RSEQC:RSEQC_READDISTRIBUTION
26 5
BAM_RSEQC:RSEQC_READDUPLICATION
27 4
QC_WORKFLOW:SEQTOOL_QC
24 2
QC_WORKFLOW:SEQTOOL_WHOLE_BAM_SATURATION
26
QC_WORKFLOW:SEQTOOL_TO_MULTIQC
24
QC_WORKFLOW:PRESEQ_LCEXTRAP
26 10
QC_WORKFLOW:PRESEQ_TO_MULTIQC
25
RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE
15 5
RNA_CONTAMINATION_DETECTION_WORKFLOW:EXTRACT_VAF_FEATURES
15
RNA_CONTAMINATION_DETECTION_WORKFLOW:PREDICT_CONTAMINATION
15
RNAFUSION:CONTAMINATION_SKIPPED_LOW_READS
11
RNAFUSION:CONTAMINATION_TO_MULTIQC
14
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