Nextflow Pipeline for processing scMTR-seq (single-cell Multi-Targets and mRNA sequencing) data

Usage with test data: ``` ./nfmtrseq -bg --type dna --genome GRCh38 --condition bulk --outdir testbulkresults data/test.HISTBulkD0fq.gz ./nfmtrseq -bg --type dna --genome GRCh38 --condition paired --outdir testpairedresults data/test.HISTDS1_.fq.gz ./nfmtrseq -bg --type dna --genome GRCh38 --condition stringent --outdir teststringentresults data/test.HISTDS1*.fq.gz ./nfmtrseq -bg --type dna --genome GRCh38 --condition relax --outdir testrelaxresults data/test.HISTHISTDS1_*.fq.gz

./nfmtrseq -bg --type rna --genome GRCh38 --condition stringent --outdir testrna data/test.SLX23062AGTTCCGTAAGGAGHISTRS1S1L001_R*.fq.gz ```

Dependencies (versions listed are those used during development of the pipeline):

• nextflow (v23.10.1)
  
• samtools (v1.19.2)
  
• bowtie (v1.3.1)
  
• bowtie2 (v2.5.3)
  
• star (2.7.11b)
  
• fastqc (v0.12.1)
  
• trim_galore (v0.6.10)
  
• python (v3.12.2)
  
• bedtools (v2.31.0)
  
• perl (v5.32.1)
  
• reachtools https://zenodo.org/doi/10.5281/zenodo.13833575
  

Here is a graphical representation of the workflow: ``` --- REACHTOOLSCOMBINE | --- TRIMGALORE (if condition == "stringent" or "paired" ) else straight to BOWTIEBC | --- BOWTIEBC - Map barcodes with bowtie | --- SAMTOFASTQ or SAMTOCOVFASTQPAIRED to convert mapped barcodes back to fastq | --- TRIMGALORE | subworkflow --- { RNA } | --- STAR | --- RNAMAPPROCESS (sub workflow) --- REACHTOOLSRMDUP2 | --- SAMTOOLSINDEX --- ADDBAMCBTAG | --- BAM2COUNTMATRIX/BAM2COUNTMATRIXSPARSE --- BAM2BED | --- READSQCEXTRACTBC --- SUMMARIZEMAPPEDREADCELLS
--- { DNA } | --- BOWTIE2 | --- SAMTOOLS SORT (+ filter if condition == "stringent") | subworkflows --- { DNAPAIREDBULK } (if condition == "paired" or "bulk" ) | --- SUMMARIZEMAPPEDREADCELLS --- REACHTOOLSRMDUP2 | --- SAMTOOLSSORTFILT | --- BAM2BED | --- FILTERREADS | --- READSQCEXTRACTBC | --- SORTDEDUP

                            --- DNA_STRINGENT_RELAX (if condition == "stringent" or "relax")
                                |
                                --- SUMMARIZE_MAPPED_READ_CELLS
                                --- REACHTOOLS_RMDUP2
                                    |
                                    --- SAMTOOLS INDEX
                                        |
                                        --- BAM2BED
                                            |
                                            --- READS_QC_EXTRACT_BC
                                                |
                                                --- COUNT_PILEUPS
                                                    |
                                                    --- REMOVE_PILEUPS
                                                        |
                                                        --- SAMTOOLS_INDEX2
                                                            |
                                                            --- BAM2BED2
                                                                |
                                                                --- READS_QC_EXTRACT_BC2

```

A previous version of this pipeline can be found here: https://github.com/laurabiggins/nfyangwang

Citation: Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq. Yang Wang, Jingyu Li, Andrew A. Malcolm, William Mansfield, Stephen J. Clark, Ricard Argelaguet, Laura Biggins, Richard Acton, Simon Andrews, Wolf Reik, Gavin Kelsey, Peter J. Rugg-Gunn