Install requirements

mamba create -n longcallR_nf_env python=3.9 -y
mamba activate longcallR_nf_env

# install PyTorch gpu version (pytorch>=1.3)
mamba install pytorch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 pytorch-cuda=12.4 -c pytorch -c nvidia -y
# or install PyTorch cpu version (pytorch>=1.3)
mamba install pytorch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 cpuonly -c pytorch -y

mamba install nextflow pysam longcallr_nn isoquant whatshap minimap2 samtools bcftools tabix -y

Quick Run

Before running this pipeline, make sure that Nextflow is installed. This workflow contains several steps:

• minimap2 alignment
• calling variants using longcallR-nn (Whole chromosome)
• calling variants using longcallR-nn + longcallR, phasing (Whole chromosome)
• calling variants using longcallR-nn + longcallR, phasing (Exon)
• calling variants only using longcallR, phasing (Whole chromosome)
• transcript analysis with IsoQuant

Clone the repo

git clone https://github.com/huangnengCSU/longcallR-nf.git
cd longcallR-nf

run from reads file

nextflow run main.nf \
-with-trace trace.txt \
--sample_name sample1 \   # input sample name
--reads /path/to/flnc.fastq \   # support multiple reads like "reads1.fastq,reads2.fastq"
--ref /path/to/ref.fa \
--platform pb \ # choice: pb/ont
--datatype masseq \ # for pb: masseq/isoseq, for ont: cDNA/dRNA
--outdir /path/to/outdir \
--annotation /path/to/gencode.v44.annotation.gtf \  # only support for gtf file, isoquant has issue with gff3 file
--threads 50 \
--threads_per_job 2 \   # setting of threads pools
--no_cuda true  # true for cpu mode and false for gpu mode

run from bam file

nextflow run main.nf \
-with-trace trace.txt \
--sample_name sample1 \   # input sample name
--bam /path/to/aln.sort.bam \
--ref /path/to/ref.fa \
--platform pb \ # choice: pb/ont
--datatype masseq \ # for pb: masseq/isoseq, for ont: cDNA/dRNA
--outdir /path/to/outdir \
--annotation /path/to/gencode.v44.annotation.gtf \  # only support for gtf file, isoquant has issue with gff3 file
--threads 50 \
--threads_per_job 2 \   # setting of threads pools
--no_cuda true  # true for cpu mode and false for gpu mode