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Use staged blacklist file in makeGenomeFilter #47

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merged 6 commits into from
Sep 30, 2019
Merged

Use staged blacklist file in makeGenomeFilter #47

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d5db29c
Merge pull request #24 from nf-core/dev
drpatelh Mar 5, 2019
c65bf6c
Merge pull request #29 from nf-core/dev
apeltzer Apr 9, 2019
b2b8af7
Add Zenodo doi
drpatelh Jun 5, 2019
c8d57b5
Merge pull request #38 from nf-core/doi
apeltzer Jun 5, 2019
efaf08a
Use staged blacklist file in makeGenomeFilter
jinmingda Sep 28, 2019
2ffcd46
Make sure channel variable blacklist is declared
jinmingda Sep 28, 2019
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8 changes: 8 additions & 0 deletions README.md
100755 → 100644
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Expand Up @@ -6,6 +6,7 @@

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
[![Docker](https://img.shields.io/docker/automated/nfcore/atacseq.svg)](https://hub.docker.com/r/nfcore/atacseq)
[![DOI](https://zenodo.org/badge/156259074.svg)](https://zenodo.org/badge/latestdoi/156259074)

### Introduction

Expand Down Expand Up @@ -74,3 +75,10 @@ The pipeline was developed by [Harshil Patel](mailto:[email protected]).
The [nf-core/rnaseq](https://github.com/nf-core/rnaseq) and [nf-core/chipseq](https://github.com/nf-core/chipseq) pipelines developed by Phil Ewels were initially used as a template for this pipeline. Many thanks to Phil for all of his help and advice, and the team at SciLifeLab.

Many thanks to others who have helped out along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@sven1103](https://github.com/sven1103), [@MaxUlysse](https://github.com/MaxUlysse), [@micans](https://github.com/micans), [@pditommaso](https://github.com/pditommaso).

## Citation

If you use nf-core/atacseq for your analysis, please cite it using the following doi: [10.5281/zenodo.2634132](https://doi.org/10.5281/zenodo.2634132)

You can cite the `nf-core` pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
5 changes: 4 additions & 1 deletion main.nf
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Expand Up @@ -219,6 +219,8 @@ if (params.blacklist) {
blacklist = Channel
.fromPath(params.blacklist, checkIfExists: true)
.ifEmpty { exit 1, "Blacklist file not found: ${params.blacklist}" }
} else {
blacklist = Channel.empty()
}

////////////////////////////////////////////////////
Expand Down Expand Up @@ -451,6 +453,7 @@ process makeGenomeFilter {

input:
file fasta from fasta_genome_filter
file blacklist from blacklist

output:
file "$fasta" into genome_fasta // FASTA FILE FOR IGV
Expand All @@ -461,7 +464,7 @@ process makeGenomeFilter {
genome_sizes_mrep_bigwig

script:
blacklist_filter = params.blacklist ? "sortBed -i ${params.blacklist} -g ${fasta}.sizes | complementBed -i stdin -g ${fasta}.sizes" : "awk '{print \$1, '0' , \$2}' OFS='\t' ${fasta}.sizes"
blacklist_filter = params.blacklist ? "sortBed -i ${blacklist} -g ${fasta}.sizes | complementBed -i stdin -g ${fasta}.sizes" : "awk '{print \$1, '0' , \$2}' OFS='\t' ${fasta}.sizes"
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Suggested change
blacklist_filter = params.blacklist ? "sortBed -i ${blacklist} -g ${fasta}.sizes | complementBed -i stdin -g ${fasta}.sizes" : "awk '{print \$1, '0' , \$2}' OFS='\t' ${fasta}.sizes"
blacklist_filter = params.blacklist ? "sortBed -i $blacklist -g ${fasta}.sizes | complementBed -i stdin -g ${fasta}.sizes" : "awk '{print \$1, '0' , \$2}' OFS='\t' ${fasta}.sizes"

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Should be fine without the '{}'.

name_filter = params.mito_name ? "| awk '\$1 !~ /${params.mito_name}/ {print \$0}'": ""
mito_filter = params.keepMito ? "" : name_filter
"""
Expand Down