Group Nextflow Assignment

Assignment Description

Produce a working Hi-C nextflow script based off of the NF-core Hi-C pipeline steps and also include a singularity container for reproducibility. https://github.com/nf-core/hic

Note: all code is strongly based off of the nf-core Hi-C script linked

Description of files for runnning Hi-C

1. Nextflow Script

'hi-c.nf' Runs Hi-C analysis in conjunction with Singularity container. Sample input FASTQ files present for test run.

Nextflow Dependency Files

1.1 FASTQ Input Samples

For use in the Hi-C pipeline to produce an output Test dataset reference source: https://github.com/nf-core/test-datasets/tree/hic

1.2 Alignment scripts

align.nf -Run “align.nf” to do Step 1 of the pipeline (mapping using a two steps strategy to rescue reads spanning the ligation sites).

1.3 Python Merging Script

mergeSAM.py (any other required python scripts) -"mergeSAM.py" merges the SAM files (which have undergone the 2-step alignment) into one paired-end BAM file – the final output of Step 1. This script and others located here: https://github.com/nf-core/hic/blob/master/bin.

1.4 NF Step one Output File Dependency

Final output file of step 1 is ${sample}_bwt2pairs.bam (SRR4292758_00_bwt2pairs.bam).

2. Singularity Container Directories and Descriptions

Base availability: Dockerfile and environment YAML: https://github.com/nf-core/hic

Modified: Index files placed in '/results/index' directory, all other files are placed in '/results/align' directory. '/data' directory: contains the raw fastq.gz files (SRR4292758_00_R1.fastq.gz, SRR4292758_00_R2.fastq.gz) '/reference' directory: contains the reference genome (W303_SGD_2015_JRIU00000000.fsa). N.B. - reference used to be .fsa.txt