WB_RNAseq-nf

nf RNA-seq pipelines for Wormbase Parasite and Vectorbase species

Nextflow scripts

• WB-se.nf (WBP species single-end reads)
• WB-pe.nf (WBP species paired-end reads)
• Ae-pe.nf (Aedes aegypti paired-end reads)

Nextflow config files

• chtc.config (UW CHTC server in Docker environment)
• chtc-local.config (local CHTC troubleshooting in Docker environment)
• brc.config (UW BRC server)

Output dirs and files

• /trim_stats/: read trimming log files
• /fastqc/: post-trimming fastqc and multiqc outputs
• /expression/: HISAT2 outputs and log files
• /bams/: sorted .bam files
• /counts/: Stringtie gene and transcript count matrices
• /align_qc/: read distribution stats
• /trace/: Nextflow timeline, report, and trace files

Example of WBP pipeline command

• WBP pipelines download and index required genomes.

nextflow run -resume [WB-pe.nf|WB-se.nf] [nextflow options] --dir [fastq dir] --release "WBPS14" --species "brugia_malayi" --prjn "PRJNA10729" --rlen "100"

Example of VB pipeline command

• VB pipelines use pre-indexed genomes.

nextflow run -resume Ae-pe.nf [nextflow options] --dir [fastq dir] --rlen "100"