BEDTOOLS_GENOMECOV_FW:
  bedtools: 2.31.1
BRACKEN:
  bracken: 2.9
CUSTOM_GETCHROMSIZES:
  getchromsizes: 1.21
CUSTOM_TX2GENE:
  python: 3.10.4
DESEQ2_QC_PSEUDO:
  r-base: 4.0.3
  bioconductor-deseq2: 1.28.0
DESEQ2_QC_STAR_SALMON:
  r-base: 4.0.3
  bioconductor-deseq2: 1.28.0
DUPRADAR:
  bioconductor-dupradar: 1.32.0
FASTP:
  fastp: 0.23.4
FASTQC_RAW:
  fastqc: 0.12.1
FASTQC_TRIM:
  fastqc: 0.12.1
FQ_LINT:
  fq: 0.12.0 (2024-07-08)
GTF2BED:
  perl: 5.26.2
KRAKEN2:
  kraken2: 2.1.3
  pigz: 2.8
MAKE_TRANSCRIPTS_FASTA:
  rsem: 1.3.1
  star: 2.7.10a
PICARD_MARKDUPLICATES:
  picard: 3.1.1
QUALIMAP_RNASEQ:
  qualimap: 2.3
RSEQC_BAMSTAT:
  rseqc: 5.0.2
RSEQC_INFEREXPERIMENT:
  rseqc: 5.0.2
RSEQC_JUNCTIONANNOTATION:
  rseqc: 5.0.2
RSEQC_JUNCTIONSATURATION:
  rseqc: 5.0.2
RSEQC_READDUPLICATION:
  rseqc: 5.0.2
SALMON_QUANT:
  salmon: 1.10.3
SAMTOOLS_FLAGSTAT:
  samtools: 1.21
SAMTOOLS_IDXSTATS:
  samtools: 1.21
SAMTOOLS_INDEX:
  samtools: 1.21
SAMTOOLS_SORT:
  samtools: 1.21
SAMTOOLS_STATS:
  samtools: 1.21
SE_GENE:
  bioconductor-summarizedexperiment: 1.32.0
SORTMERNA:
  sortmerna: 4.3.7
SORTMERNA_INDEX:
  sortmerna: 4.3.7
STAR_ALIGN:
  star: 2.7.11b
  samtools: 1.21
  gawk: 5.1.0
STRINGTIE_STRINGTIE:
  stringtie: 2.2.3
TXIMETA_TXIMPORT:
  bioconductor-tximeta: 1.20.1
UCSC_BEDCLIP:
  ucsc: 377
UCSC_BEDGRAPHTOBIGWIG:
  ucsc: 469
Workflow:
    nf-core/rnaseq: v3.18.0-gb96a753
    Nextflow: 24.10.5