README.md

Nextflow NME pipelines

Nextflow pipelines available for the NME users in the ETH Zürich Euler cluster.

The pipelines were adapted from the repository https://github.com/s-andrews/nextflow_pipelines from the The Babraham Institute.

Alignment

📁 nf_bowtie2
📁 nf_hisat2

ChIP-seq or CutnTag

📁 nf_chipseq
📁 nf_cutntag
📁 nf_peakcalling

RNA-seq

📁 nf_rnaseq

Processing and quality control

📁 nf_qc
📁 nf_fastq_screen
📁 nf_fastqc
📁 nf_trim_galore
📁 nf_sortIndexBAM
📁 nf_umibam

Methylation sequencing

📁 nf_bismark
📁 nf_bisulfite_PBAT
📁 nf_bisulfite_PBAT_DirtyHarry
📁 nf_bisulfite_RRBS
📁 nf_bisulfite_RRBS_clock
📁 nf_bisulfite_WGBS
📁 nf_bisulfite_scBSseq

Nucleosome, Methylation and Transcription sequencing

📁 nf_bisulfite_scNMT