CRC atlas - velocyto nextflow pipeline

#TODO: documentation

1.1. Usage

$ nextflow run main.nf -profile cluster,conda

<Arguments>

--input_csv = path to the input CSV file (see below for details)

--gtf_file = path to GTF file (used for the creation of the BAM files)

--masked_repeats = path to the masked repeats file

--out_dir = path to the output directory

--publish_dir_mode = mode of publishDir directive (default: "copy")

--run_10x = run velocyto run10x command on the samples (default: false - see Note below for details)

Notes

**Outpur directory

The pipeline will output the results in the /path/to/Sample.bam directory by default. You need to specify a directory through --out_dir otherwise.

CSV file (default settings)

study,sample_id,bam,bcl
cohort_1,sample_1,/path/to/Sample1_possorted.bam,/path/to/Sample1_barcodes.tsv
cohort_2,sample_2,/path/to/Sample2_possorted.bam,/path/to/Sample2_barcodes.tsv

• If you choose the --run_10x true you need to change the input CSV file to specify the cellranger directories instead of specific bam files (not tested yet)

CSV file (run_10x flag)

study,sample_id,bam
cohort_1,sample_1,/path/to/Sample1/
cohort_2,sample_2,/path/to/Sample2/