Processes

NFCORE_RNAFUSION:GENERATE_SAMPLE_TYPE_MAP
1
DEMULTIPLEX:BCLCONVERT
8
DEMULTIPLEX:FLOWCELL_QC
1
DEMULTIPLEX:AGGREGATE_DEMUX_STATS
1
DEMULTIPLEX:SAMPLESHEET_CHECK
1
DEMULTIPLEX:CAT_FASTQ
96
DEMULTIPLEX:SAMPLESHEET_FROM_MERGED
1
RNAFUSION:FASTQC
52 44
TRIM_WORKFLOW:FASTP
96
TRIM_WORKFLOW:FASTQC_FOR_FASTP
50 46 1
RNAFUSION:KALLISTO_INDEX
1
RNAFUSION:KALLISTO_QUANT
42 54 1
RNAFUSION:KALLISTO_TO_TX2GENE_QC
42
RNAFUSION:KALLISTO_TO_MULTIQC
42
RNAFUSION:GTF2BED
1
FASTQ_ALIGN_STAR:STAR_ALIGNMENT
37 59 2
FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT
35 2
RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM
28 7
RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM
27 1
ARRIBA_WORKFLOW:ARRIBA
29 8
ARRIBA_WORKFLOW:ARRIBA_FILTER
28 1
STARFUSION_WORKFLOW:STARFUSION
17 20 1
STARFUSION_WORKFLOW:STARFUSION_FILTER
15 2
FUSIONREPORT_WORKFLOW:FUSIONREPORT
13
FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR
1 4 3
FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV
FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT
FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION
RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS
28 7
RNAFUSION:CANCER_INTRONS_TO_VCF
28
QC_WORKFLOW:GATK4_MARKDUPLICATES
8 29
QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS
QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS
BAM_RSEQC:RSEQC_BAMSTAT
18 17 1
BAM_RSEQC:RSEQC_INNERDISTANCE
34 1
BAM_RSEQC:RSEQC_INFEREXPERIMENT
34 1
BAM_RSEQC:RSEQC_JUNCTIONANNOTATION
20 15 2
BAM_RSEQC:RSEQC_JUNCTIONSATURATION
21 14
BAM_RSEQC:RSEQC_READDISTRIBUTION
15 20
BAM_RSEQC:RSEQC_READDUPLICATION
14 21
QC_WORKFLOW:SEQTOOL_QC
5 3
QC_WORKFLOW:SEQTOOL_WHOLE_BAM_SATURATION
7 1
QC_WORKFLOW:RSEQC_TO_MULTIQC
16 2
QC_WORKFLOW:SEQTOOL_TO_MULTIQC
5
QC_WORKFLOW:PRESEQ_LCEXTRAP
14 23
QC_WORKFLOW:PRESEQ_TO_MULTIQC
11 3
RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE
21 12
RNA_CONTAMINATION_DETECTION_WORKFLOW:EXTRACT_VAF_FEATURES
21
RNA_CONTAMINATION_DETECTION_WORKFLOW:PREDICT_CONTAMINATION
20
RNAFUSION:CONTAMINATION_SKIPPED_LOW_READS
2
RNAFUSION:CONTAMINATION_TO_MULTIQC
19
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