Basic nf-core run examples

1. nf-core/rnaseq

nextflow run nf-core/rnaseq -profile docker --input samplesheet.csv

STEPs in RNAseq workflow

FastQC
UMI-tools extract
TrimGalore
fastp
BBSplit
SortMeRNA
STAR or Salmon
RSEM
HISAT2

nf-core/rnaseq

2. nf-core/methylseq

nextflow run nf-core/methylseq -profile docker --input '*_R{1,2}.fastq.gz'

STEPs in Bismark workflow

Merge re-sequenced FastQ files : cat
Raw data QC : FastQC
Adapter sequence trimming : Trim Galore!
Align Reads : Bismark
Deduplicate Alignments : Bismark
Extract methylation calls : Bismark
Sample report : Bismark
Summary Report : Bismark
Alignment QC : Qualimap
Sample complexity : Preseq
Project Report : MultiQC

Input File samplesheet.csv :
sample,fastq_1,fastq_2
samplename, fastq1, fastq2 

nextflow run nf-core/methylseq --input samplesheet.csv 
                               --outdir results 
                               --genome GRCh37 
                               -profile docker 
                               -c my_custom_config.nf

-profile run environment
-c additional parameters

-profile options
docker
conda

nf-core/methylseq link


3. nf-core/sarek

To detect SNP, Indel, SV, CNV.

Alternative to nf-core/exoseq (no longer maintained)

nextflow run nf-core/sarek -profile docker --input samples.tsv

Additional reading : snakemake-exome
link

4. nf-core/chipseq

nextflow run nf-core/chipseq -profile docker --input design.csv

5. nf-core/atacseq

nextflow run nf-core/atacseq -profile docker --input design.csv

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