This repository contains a Nextflow based DNA/RNA data processing pipeline built specifically for Meltzer lab. This pipeline is built to run variant filtering and extensive QC on a sequencing run. The pipeline supports processing data from multiple references. We currently support
| Genome | Version |
|---|---|
| Human | hg19, hg38 |
| Mouse | mm10, mm39 |
| Dog | canFam3, canFam6 |
This pipeline is developed and deployed solely on NIH Biowulf.
This pipeline is hosted under /data/GBNCI directory. You'll need to start an interactive session inorder to launch the pipeline.
sinteractive --mem=30g --cpus-per-task=4
Usage: /data/GBNCI/MeltzerLab_Nextflow_pipeline/nf.sh <samplesheet>
This script requires one positional argument:
<samplesheet>: Provide the full path to the samplesheet in a Meltzer lab accepted format.
eg: /data/GBNCI/MeltzerLab_Nextflow_pipeline/nf.sh /data/GBNCI/DATA/VG_test/samplesheet.tsv
Input file is a tab seperated samplesheet file from Meltzer lab. However the pipeline can be launched as long as these columns are present. Here is an example of the expected format.
| flowcell | library | sample_type | genome | read1 | read2 | capture_targets |
|---|---|---|---|---|---|---|
| AAZ123 | L080123_RNA | Total RNA | hg19 | L080123_RNA_R1.fastq.gz | L080123_RNA_R1.fastq.gz | APC_TP53_BAC_KlenowBait |
Come across a bug? Open an issue and include a minimal reproducible example.
Have a question? Ask it in discussions.
Want to contribute to this project? Check out the contributing guidelines.
This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool1 and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions2.
Footnotes
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instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core ↩