scAnnotatiONT tool and pipeline

Introduction

Step	Tool	Input	Output
1. Construct novel annotation	StringTie2 Scallop	`BAM` `GTF`	`GTF`
2. Merge novel and reference annotations	cuffmerge	`GTF`	`GTF`
3. Compare novel annotations with reference	GffCompare	`GTF`	`summary.txt`
4. Extract more statistics from novel annotation	Rscript	`GTF`	`report_stats_annotation.txt`
5. Build UCSC trackhub	bash script	`BAM` `GTF`	`UCSC trackhub folder` `bigWig` `bigGenePred`
6. Assign reads to genes	featureCounts	`BAM` `GTF`	`BAM`
7. Sort and index BAM file	Samtools	`BAM`	`BAM` `BAI`
8. Count unique reads per genes per cell	UMI-tools	`BAM`	`count_matrix.txt`
9. Run MultiQC	MultiQC	`BAM` `GTF`	`multiqc_report.html`

$ nextflow run . -profile singularity --threads 4 --output output

Option	Description
`help`	Display help message
`threads`	Number of threads to use for each process
`output`	Directory to write output files to