Processes

COPY_INPUT_TO_OUTDIR
1
RNAFUSION:CAT_FASTQ
RNAFUSION:FASTQC
2
TRIM_WORKFLOW:FASTP
2
TRIM_WORKFLOW:FASTQC_FOR_FASTP
2
RNAFUSION:KALLISTO_INDEX
1
RNAFUSION:KALLISTO_QUANT
2
RNAFUSION:KALLISTO_TO_TX2GENE_QC
2
RNAFUSION:KALLISTO_TO_MULTIQC
2
RNAFUSION:GTF2BED
1
FASTQ_ALIGN_STAR:STAR_ALIGNMENT
2
FASTQ_ALIGN_STAR:SAMTOOLS_INDEX_STAR_ALIGNMENT
2
RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM
2
RNAFUSION:SAMTOOLS_INDEX_ALIGNMENT_CRAM
2
ARRIBA_WORKFLOW:ARRIBA
2
ARRIBA_WORKFLOW:ARRIBA_FILTER_SAME_GENE
2
STARFUSION_WORKFLOW:STARFUSION
2 1
STARFUSION_WORKFLOW:STARFUSION_FILTER
2
FUSIONREPORT_WORKFLOW:FUSIONREPORT
2
FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR
2
FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV
2
FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT
2
FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION
2
RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS
2
RNAFUSION:CANCER_INTRONS_TO_VCF
2
QC_WORKFLOW:GATK4_MARKDUPLICATES
2
QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS
2
QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS
2
BAM_RSEQC:RSEQC_BAMSTAT
2
BAM_RSEQC:RSEQC_INNERDISTANCE
2
BAM_RSEQC:RSEQC_INFEREXPERIMENT
2
BAM_RSEQC:RSEQC_JUNCTIONANNOTATION
2
BAM_RSEQC:RSEQC_JUNCTIONSATURATION
2
BAM_RSEQC:RSEQC_READDISTRIBUTION
2
BAM_RSEQC:RSEQC_READDUPLICATION
2
QC_WORKFLOW:SEQTOOL_QC
2
QC_WORKFLOW:SEQTOOL_WHOLE_BAM_SATURATION
2
QC_WORKFLOW:SEQTOOL_TO_MULTIQC
2
QC_WORKFLOW:PRESEQ_LCEXTRAP
2
QC_WORKFLOW:PRESEQ_TO_MULTIQC
2
RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE
2
RNA_CONTAMINATION_DETECTION_WORKFLOW:EXTRACT_VAF_FEATURES
2
RNA_CONTAMINATION_DETECTION_WORKFLOW:PREDICT_CONTAMINATION
2
RNAFUSION:CONTAMINATION_SKIPPED_LOW_READS
RNAFUSION:CONTAMINATION_TO_MULTIQC
2
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_METRICS
1