Sample	bedtools	getchromsizes	python	r-base	bioconductor-deseq2	bioconductor-dupradar	fastqc	fq	perl	rsem	star	picard	qualimap	rseqc	salmon	samtools	bioconductor-summarizedexperiment	gawk	stringtie	bioconductor-tximeta	ucsc	nf-core/rnaseq	Nextflow
BEDTOOLS_GENOMECOV_FW	2.31.1																						
CUSTOM_GETCHROMSIZES		1.21																					
CUSTOM_TX2GENE			3.10.4																				
DESEQ2_QC_STAR_SALMON				4.0.3	1.28.0																		
DupRadar						1.32.0																	
FASTQC							0.12.1																
FQ_LINT								0.12.0 (2024-07-08)															
FQ_SUBSAMPLE								0.12.0 (2024-07-08)															
GTF2BED									5.26.2														
GTF_FILTER			3.9.5																				
MAKE_TRANSCRIPTS_FASTA										1.3.1	2.7.10a												
PICARD_MARKDUPLICATES												3.1.1											
QUALIMAP_RNASEQ													2.3										
RSEQC_BAMSTAT														5.0.2									
RSEQC_INFEREXPERIMENT														5.0.2									
RSEQC_INNERDISTANCE														5.0.2									
RSEQC_JUNCTIONANNOTATION														5.0.2									
RSEQC_JUNCTIONSATURATION														5.0.2									
RSEQC_READDISTRIBUTION														5.0.2									
RSEQC_READDUPLICATION														5.0.2									
SALMON_INDEX															1.10.3								
SALMON_QUANT															1.10.3								
SAMTOOLS_FLAGSTAT																1.21							
SAMTOOLS_IDXSTATS																1.21							
SAMTOOLS_INDEX																1.21							
SAMTOOLS_SORT																1.21							
SAMTOOLS_STATS																1.21							
SE_GENE																	1.32.0						
STAR_ALIGN											2.7.11b					1.21		5.1.0					
STAR_GENOMEGENERATE											2.7.11b					1.21		5.1.0					
STRINGTIE_STRINGTIE																			2.2.3				
TXIMETA_TXIMPORT																				1.20.1			
UCSC_BEDCLIP																					377		
UCSC_BEDGRAPHTOBIGWIG																					469		
Workflow																						v3.18.0-gb96a753	24.10.5