software_versions_salmon.yml

BEDTOOLS_GENOMECOV:
  bedtools: 2.30.0
CUSTOM_DUMPSOFTWAREVERSIONS:
  python: 3.10.6
  yaml: "6.0"
CUSTOM_GETCHROMSIZES:
  getchromsizes: 1.16.1
DESEQ2_QC_SALMON:
  bioconductor-deseq2: 1.28.0
  r-base: 4.0.3
DESEQ2_QC_STAR_SALMON:
  bioconductor-deseq2: 1.28.0
  r-base: 4.0.3
DUPRADAR:
  bioconductor-dupradar: 1.28.0
  r-base: 4.2.1
FASTQC:
  fastqc: 0.11.9
GTF_GENE_FILTER:
  python: 3.9.5
MAKE_TRANSCRIPTS_FASTA:
  rsem: 1.3.1
  star: 2.7.10a
MULTIQC_CUSTOM_BIOTYPE:
  python: 3.9.5
PICARD_MARKDUPLICATES:
  picard: 2.27.4-SNAPSHOT
QUALIMAP_RNASEQ:
  qualimap: 2.2.2-dev
RSEQC_BAMSTAT:
  rseqc: 3.0.1
RSEQC_INFEREXPERIMENT:
  rseqc: 3.0.1
RSEQC_INNERDISTANCE:
  rseqc: 3.0.1
RSEQC_JUNCTIONANNOTATION:
  rseqc: 3.0.1
RSEQC_JUNCTIONSATURATION:
  rseqc: 3.0.1
RSEQC_READDISTRIBUTION:
  rseqc: 3.0.1
RSEQC_READDUPLICATION:
  rseqc: 3.0.1
SALMON_INDEX:
  salmon: 1.9.0
SALMON_QUANT:
  salmon: 1.9.0
SALMON_SE_GENE:
  bioconductor-summarizedexperiment: 1.24.0
  r-base: 4.1.1
SALMON_TX2GENE:
  python: 3.9.5
SALMON_TXIMPORT:
  bioconductor-tximeta: 1.12.0
  r-base: 4.1.1
SAMPLESHEET_CHECK:
  python: 3.9.5
SAMTOOLS_FLAGSTAT:
  samtools: 1.16.1
SAMTOOLS_IDXSTATS:
  samtools: 1.16.1
SAMTOOLS_INDEX:
  samtools: 1.16.1
SAMTOOLS_SORT:
  samtools: 1.16.1
SAMTOOLS_STATS:
  samtools: 1.16.1
STAR_ALIGN_IGENOMES:
  gawk: 5.1.0
  samtools: "1.10"
  star: 2.6.1d
STRINGTIE_STRINGTIE:
  stringtie: 2.2.1
SUBREAD_FEATURECOUNTS:
  subread: 2.0.1
TRIMGALORE:
  cutadapt: "3.4"
  trimgalore: 0.6.7
UCSC_BEDCLIP:
  ucsc: "377"
UCSC_BEDGRAPHTOBIGWIG:
  ucsc: "377"
Workflow:
  Nextflow: 22.10.4
  nf-core/rnaseq: 3.10.1