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Nextflow

Nextflow

Nextflow is a pl created in 2013.

#209on PLDB 9Years Old 3.3kUsers
0Books 1Papers 3kRepos

A DSL for data-driven computational pipelines


Example from Linguist:
#!/usr/bin/env nextflow /* * This is free and unencumbered software released into the public domain. * * Anyone is free to copy, modify, publish, use, compile, sell, or * distribute this software, either in source code form or as a compiled * binary, for any purpose, commercial or non-commercial, and by any * means. * * In jurisdictions that recognize copyright laws, the author or authors * of this software dedicate any and all copyright interest in the * software to the public domain. We make this dedication for the benefit * of the public at large and to the detriment of our heirs and * successors. We intend this dedication to be an overt act of * relinquishment in perpetuity of all present and future rights to this * software under copyright law. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. * IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR * OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, * ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR * OTHER DEALINGS IN THE SOFTWARE. * * For more information, please refer to <http://unlicense.org/> */ /* * Author Paolo Di Tommaso <paolo.ditommaso@gmail.com> */ params.query = "$HOME/sample.fa" params.db = "$HOME/tools/blast-db/pdb/pdb" process blast { output: file top_hits """ blastp -query ${params.query} -db ${params.db} -outfmt 6 \ | head -n 10 \ | cut -f 2 > top_hits """ } process extract { input: file top_hits output: file sequences """ blastdbcmd -db ${params.db} -entry_batch $top_hits > sequences """ } process align { input: file sequences echo true """ t_coffee $sequences 2>&- | tee align_result """ }

Language features

Feature Supported Example Token
Comments
/* A comment
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MultiLine Comments
/* A comment
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/* */
Semantic Indentation ϴ

Publications about Nextflow from Semantic Scholar

title authors year citations influentialCitations
DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines Alper Kucukural and Manuel Garber and O. Yukselen and Osman Turkyilmaz and A. Ozturk and Isabelle Girard and Roy Martin 2019 2 0
newlisp.html · nextflow.html · qml.html

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