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事例紹介: Nextflow in ワークショップ「なぜ我々はワークフロー言語を書くのか」

Haruka Ozaki
September 27, 2021

事例紹介: Nextflow in ワークショップ「なぜ我々はワークフロー言語を書くのか」

2021/09/27 IIBMP2021
ワークショップ「なぜ我々はワークフロー言語を書くのか」
事例紹介: Nextflow

Haruka Ozaki

September 27, 2021
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  1. #!/usr/bin/env nextflow params.in = "$baseDir/data/sample.fa" // split a fasta file

    in multiple files process splitSequences { input: path 'input.fa' from params.in output: path 'seq_*' into records """ awk '/^>/{f="seq_"++d} {print > f}' < input.fa """ } // Simple reverse the sequences process reverse { input: path x from records output: stdout into result """ cat $x | rev """ } /FYUGMPXͷߏ੒ཁૉɿ1SPDFTTͱ$IBOOFM 4 Process ɾೖྗɺܭࢉɺग़ྗΛ ɹهड़ Channel ɾೖग़ྗσʔλ͕௨Δ ɹʮྲྀ࿏ʯΛهड़
  2. #!/usr/bin/env nextflow params.in = "$baseDir/data/sample.fa" // split a fasta file

    in multiple files process splitSequences { input: path 'input.fa' from params.in output: path 'seq_*' into records """ awk '/^>/{f="seq_"++d} {print > f}' < input.fa """ } // Simple reverse the sequences process reverse { input: path x from records output: stdout into result """ cat $x | rev """ } /FYUGMPXͷߏ੒ཁૉɿ1SPDFTTͱ$IBOOFM 5 Process ɾೖྗɺܭࢉɺग़ྗΛ ɹهड़ Channel ɾೖग़ྗσʔλ͕௨Δ ɹʮྲྀ࿏ʯΛهड़ ೖྗ ग़ྗ ܭࢉ ೖྗ ग़ྗ ܭࢉ
  3. #!/usr/bin/env nextflow params.in = "$baseDir/data/sample.fa" // split a fasta file

    in multiple files process splitSequences { input: path 'input.fa' from params.in output: path 'seq_*' into records """ awk '/^>/{f="seq_"++d} {print > f}' < input.fa """ } // Simple reverse the sequences process reverse { input: path x from records output: stdout into result """ cat $x | rev """ } /FYUGMPXͷߏ੒ཁૉɿ1SPDFTTͱ$IBOOFM 6 Process ɾೖྗɺܭࢉɺग़ྗΛ ɹهड़ Channel ɾೖग़ྗσʔλ͕௨Δ ɹʮྲྀ࿏ʯΛهड़ ೖྗ ग़ྗ ܭࢉ ೖྗ ग़ྗ ܭࢉ
  4. /(4ղੳύΠϓϥΠϯΛॻ͘ͷʹ࢖༻͍ͯ͠·͢ •nextflow run pipeline.nf w $I*1TFRղੳɺ༥߹Ҩ఻ࢠݕग़ɺ̍ࡉ ๔3/"TFRͷ6.*Χ΢ϯςΟϯάFUD w ϓϩτλΠϐϯά͔Β࢖༻ w

    ίϚϯυϥΠϯҾ਺ΛऔΕΔ ʢϑΝΠϧύεࢦఆ΍ιϑτ΢ΣΞͷΦ ϓγϣϯΛม͑ͨΓʣ w ίϯϑΟάϑΝΠϧΛ࢖͑Δ w Ϧιʔε࢖༻ྔͷϩά΋औΕΔ 9