Processes

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