Use staged blacklist file in makeGenomeFilter #47
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Dev > Master for v1.0.0 release
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Create an empty channel for blacklist when params.blacklist is false.
drpatelh
requested changes
Sep 29, 2019
| @@ -461,7 +464,7 @@ process makeGenomeFilter { | |||
| genome_sizes_mrep_bigwig | |||
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| 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 '{}'.
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Thanks @jinmingda . This is perfect. Im quite impressed with your level of knowledge of Nextflow by the way 😎 Would you mind also adding a line to |
drpatelh
approved these changes
Sep 30, 2019
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Ill make the changes in to get the PR merged 👍 |
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Many thanks to contributing to nf-core/atacseq!
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PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/atacseq/tree/master/.github/CONTRIBUTING.md
Description
The channel containing a staged blacklist file is not added to the process
makeGenomeFilter. Usingparams.blacklistwill cause an error when the pipeline is running on an environment where workers don't have access to the files stored in head node (like AWS Batch). This PR attempts to solve this problem by using the staged blacklist file from the channel input, which has been created already.