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

Transcript

1. 
   
   **#.1
   ϫʔΫγϣοϓʮͳͥզʑ͸ϫʔΫϑϩʔݴޠΛॻ͘ͷ͔ʯ
   ࣄྫ঺հ
   /FYUGMPX ඌ࡚
   ྒྷʢஜ೾େֶʣ
   ஜ೾େֶ
   ҩֶҩྍܥ
   ੜ໋ҩՊֶҬ
   όΠΦΠϯϑΥϚςΟΫεݚڀࣨ
   ஜ೾େֶ
   ਓ޻஌ೳՊֶηϯλʔ
   ཧԽֶݚڀॴ
   ੜ໋ػೳՊֶݚڀηϯλʔ !ZVJGV !P[BLJMBC
2. ϫʔΫϑϩʔʹϓϩηεͷ࿈ͳΓ w ϓϩηεʹܭࢉʢπʔϧɺεΫϦϓτʣʴೖग़ྗ
   w πʔϧ
   ιϑτ΢ΣΞɺόʔδϣϯɺΦϓγϣϯ
   w ೖग़ྗ
   ೖྗϑΝΠϧͱग़ྗϑΝΠϧ 2 ܭࢉ ϓϩηε ೖྗ σʔλ ग़ྗ σʔλ ܭࢉ ೖྗ ग़ྗ σʔλ ϓϩηε
3. /FYUGMPXͷߏ੒ཁૉɿ1SPDFTT
   ͱ
   $IBOOFM w 1SPDFTT
   ܭࢉʢπʔϧɺεΫϦϓτʣɺೖग़ྗΛهड़
   w ೖग़ྗʹ
   $IBOOFM
   Λهड़͢Δ
   w $IBOOFM
   σʔλ͕௨Δʮྲྀ࿏ʯΛهड़ 3 ܭࢉ ϓϩηε ೖྗ σʔλ ग़ྗ σʔλ ܭࢉ ೖྗ ग़ྗ σʔλ ϓϩηε
4. #!/usr/bin/env nextflow params.in = "$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੒ཁૉɿ1SPDFTT
   ͱ
   $IBOOFM 4 Process ɾೖྗɺܭࢉɺग़ྗΛ ɹهड़ Channel ɾೖग़ྗσʔλ͕௨Δ ɹʮྲྀ࿏ʯΛهड़
5. #!/usr/bin/env nextflow params.in = "$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੒ཁૉɿ1SPDFTT
   ͱ
   $IBOOFM 5 Process ɾೖྗɺܭࢉɺग़ྗΛ ɹهड़ Channel ɾೖग़ྗσʔλ͕௨Δ ɹʮྲྀ࿏ʯΛهड़ ೖྗ ग़ྗ ܭࢉ ೖྗ ग़ྗ ܭࢉ
6. #!/usr/bin/env nextflow params.in = "$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੒ཁૉɿ1SPDFTT
   ͱ
   $IBOOFM 6 Process ɾೖྗɺܭࢉɺग़ྗΛ ɹهड़ Channel ɾೖग़ྗσʔλ͕௨Δ ɹʮྲྀ࿏ʯΛهड़ ೖྗ ग़ྗ ܭࢉ ೖྗ ग़ྗ ܭࢉ
7. /FYUGMPXͷʢݸਓతʣخ͠͞ɿ$IBOOFM w ೖྗϑΝΠϧͷ਺ͳͲΛ໌ࣔతʹߟ͑ͳ͍͍ͯ͘
   w ଟ͘ͷϑΝΠϧʹฒྻʹಉ͡ܭࢉΛ
   w $IBOOFM
   ͷʮԋࢉʯ͕Ͱ͖Δ
   w σʔλ΍Φϓγϣϯͷʮ૊Έ߹ΘͤʯΛ؆୯ʹهड़Ͱ͖Δ
   w σʔλͷ໊લ΍αΠζͳͲʹΑΔʮ৚݅෼ذʯΛ؆୯ʹهड़Ͱ͖Δ 7
8. /FYUGMPXͷʢݸਓతʣخ͠͞ɿந৅తهड़ w ʮܭࢉʯͷ෦෼͸طଘͷεΫϦϓτΛྲྀ༻Ͱ͖Δ
   w CBTIɺ1ZUIPOͳͲ
   w &YFDVUPS͕࣮ߦ؀ڥͷҧ͍Λٵऩ
   w FYFDVUPS
   
   MPDBM
   FYFDVUPS
   
   THF
   ͳͲͱॻ͚Ε͹͍͍
   w ίϯςφ΍DPOEBͳͲͱͷ࿈ܞ΋؆୯
   w ˠ
   هड़ͱ࣮૷ͷ෼཭ 8
9. /(4ղੳύΠϓϥΠϯΛॻ͘ͷʹ࢖༻͍ͯ͠·͢ •nextflow run pipeline.nf w $I*1TFRղੳɺ༥߹Ҩ఻ࢠݕग़ɺ̍ࡉ ๔3/"TFRͷ6.*Χ΢ϯςΟϯά
   
   FUD
   w ϓϩτλΠϐϯά͔Β࢖༻
   w ίϚϯυϥΠϯҾ਺ΛऔΕΔ
   ʢϑΝΠϧύεࢦఆ΍ιϑτ΢ΣΞͷΦ ϓγϣϯΛม͑ͨΓʣ
   w ίϯϑΟάϑΝΠϧΛ࢖͑Δ
   w Ϧιʔε࢖༻ྔͷϩά΋औΕΔ 9
10. /FYUGMPX
    ͷকདྷɿهड़ͱ࣮૷ͷ͞ΒͳΔ෼཭ w /FYUqPX
    UPXFS
    w (6*
    w ༷ʑͳΫϥ΢υ؀ڥ΁ͷϫʔΫϑϩ ʔͷσϓϩΠ͕Մೳ
    w 42-ͳͲͱͷ࿈ܞ 10 https://twitter.com/PaoloDiTommaso/status/1433120149888974854