Skip to content

settings.md

Latest commit

 

History

History
43 lines (39 loc) · 2.45 KB

settings.md

File metadata and controls

43 lines (39 loc) · 2.45 KB
Raw

General pipeline settings

  • --help Display pipeline help menu (Default: false)
  • --singleEnd true/false for single-end sequencing (Default: false)
  • --unstranded true/false for unstranded library prep (Default: true)
  • --stranded true/false for forward-stranded library prep (Default: false)
  • --revstranded true/false for reverse-stranded library prep (Default: false)
  • --gencode gencode reference. Required for Salmonh indexing (Default: false).
  • --customQC Run customQC module and generate HTML report (Default: true).

featureCount quantification settings

  • --fc_group_features subread featureCounts group (Default: gene_id)
  • --fc_count_type subread subread featureCounts type (Default: exon)
  • --fc_group_features_type GTF biotype field for subread featureCounts (Default: gene_biotype)
  • --normalize_counts enable edgeR RPKM/CPM normalization for featureCounts (Default: true)
  • --biotypeQC perform featureCounts biotype quantification (Default: true).

Pipeline steps

  • --runFastQC Read QC with fastqc (Default: true)
  • --runTrimGalore Read trimming with TrimGalore (Default: true)
  • --runSortMeRNA rRNA filtering with SortMeRNA (Default: true)
  • --runPostQC Alignment QC with RSeQC,Preseq (Default: true)
  • --runRSeQC_TIN RSeQC TIN (Default: true)
  • --runMarkDup Sambamba markdup (Default: true)
  • --runFeatureCounts Expression quantification with featureCounts (Default: true)
  • --runMapping Read alignment with STAR (Default: true)
  • --runSalmon Alignment-free transcript quantification with Salmon (Default: false)
  • --runMultiQC MultiQC report (Default: true)
  • --runGermlineCallingGATK GATK4 germline variant calling (Default: false)
  • --runGATK4_BQSR GATK4 base quality score recalibration with --runGermlineCallingGATK enabled (Default: true).

Reference resources

  • --genome_fasta /path/to/reference/genome.fasta
  • --genome_index /path/to/reference/genome.fasta.fai
  • --genome_dict /path/to/reference/genome.dict
  • --genome_gtf /path/to/reference/annotation.gtf
  • --transcripts_fasta /path/to/reference/transcripts.fasta (required for Salmon)
  • --genome_bed path/to/reference/annotation.bed12
  • --star_index path/to/star_index
  • --salmon_index path/to/salmon_index
  • --genome_known_sites path/to/snp_sites.vcf (optional, GATK4 BQSR)
  • --scatter_interval_list path/to/scatter.interval_list (required for GATK4)
  • --rRNA_database_manifest path/to/rRNA database file (required for SortMeRNA)