Nextflow

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기타

nextflow는 groovy의 파생 때문에
nextflow 구문 하이라이터가없는 환경에서는,
groovy 하이라이터를 사용하는 손도 있다.

nextflow를 사용해 봅시다.

설치 등

Nextflow - A DSL for parallel and scalable computational pipelines

Java 8 이상을 넣어 둔다

curl -s https://get.nextflow.io | bash

./nextflow run hello

다운로드할 때의 로그 등

다운로드하면,
의존하는 java 라이브러리를 다운로드하는 것 같은 로그가 나옵니다.
궁극적으로 움직이는 환경이 있습니다.

다양한 데이터는 ~/.nextflow에 들어가는 것 같습니다.

설치가 끝나면 로그

CAPSULE: Downloading dependency commons-codec:commons-codec:jar:1.10

N E X T F L O W
version 19.04.1 build 5072
last modified 03-05-2019 12:29 UTC (21:29 JDT)
cite doi:10.1038/nbt.3820
http://nextflow.io


Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: /Users/manabu/work/nextflow
- you may complete the installation by moving it to a directory in your $PATH

처음 명령 실행

$ ./nextflow run hello
N E X T F L O W  ~  version 19.04.1
Pulling nextflow-io/hello ...
downloaded from https://github.com/nextflow-io/hello.git
Launching `nextflow-io/hello` [high_mayer] - revision: a9012339ce [master]
[warm up] executor > local
executor >  local (4)
[27/9839a3] process > sayHello [100%] 4 of 4 ✔
Ciao world!

Bonjour world!

Hola world!

Hello world!

Completed at: 28-Jun-2019 11:11:33
Duration    : 1.1s
CPU hours   : (a few seconds)
Succeeded   : 4

$  nextflow file nextflow
nextflow: Bourne-Again shell script text executable, ASCII text

Nextflow - Basic pipeline

샘플을 example1.nf로 저장

$  nextflow ./nextflow example1.nf
N E X T F L O W  ~  version 19.04.1
Launching `example1` [suspicious_yalow] - revision: 3c1734c90b
[warm up] executor > local
executor >  local (1)
[ab/9776d1] process > splitSequences [  0%] 0 of 1
ERROR ~ Error executing process > 'splitSequences'

executor >  local (1)
[ab/9776d1] process > splitSequences [100%] 1 of 1, failed: 1 ✘
ERROR ~ Error executing process > 'splitSequences'

Caused by:
  Process `splitSequences` terminated with an error exit status (1)

Command executed:

  awk '/^>/{f="seq_"++d} {print > f}' < input.fa

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 2: input.fa: No such file or directory

Work dir:
  /Users/manabu/work/nextflow/work/ab/9776d1a5bb20bbd2415b237cfda7d7

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

FASTA - Wikipedia

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY

실패했을 때의 오류

입력 파일을 기본값에 맞추기

$ mv data/input.fa data/sample.fa

실행합니다.
- 분해(split)한 것은 파일에 출력되어
- 반전시킨 것은 표준출력으로 출력된다

$  ./nextflow example1.nf
N E X T F L O W  ~  version 19.04.1
Launching `example1` [nauseous_mirzakhani] - revision: 3c1734c90b
[warm up] executor > local
executor >  local (2)
[43/3398fe] process > splitSequences [100%] 1 of 1 ✔
[3b/5a7487] process > reverse        [  0%] 0 of 1
]sumixam sumixam sahpelE[ b emorhcotyc |1.66144DAA|bg|1124255|ig>
VLNTGIYPIASFLNTIVTAGWFSMQGWPLVYGMFATAMTILLLMIGTNWTESYLYSGYYINRGIHTYLCL
GLFDKITYYPHFPIKDSDSTLGLPNNSGTEHLFTLHVGALAVMTFPLIFHFAFFRNLTAKDVSFGGWIWE
LIVISLFLALVGGLKNPVSRLIAYAFLFYWEPKIHLPTNLPDAPMHNDPDGLMDPSLLALLLLLLILILL
executor >  local (2)
[43/3398fe] process > splitSequences [100%] 1 of 1 ✔
[3b/5a7487] process > reverse        [100%] 1 of 1 ✔
Completed at: 28-Jun-2019 11:20:22
Duration    : 1.1s
CPU hours   : (a few seconds)
Succeeded   : 2

$ ./nextflow example1.nf
N E X T F L O W  ~  version 19.04.1
Launching `example1` [maniac_poisson] - revision: 3c1734c90b
[warm up] executor > local
executor >  local (2)
[ac/3e7150] process > splitSequences [100%] 1 of 1 ✔
[c4/de9f8e] process > reverse        [  0%] 0 of 1
]sumixam sumixam sahpelE[ b emorhcotyc |1.66144DAA|bg|1124255|ig>
VLNTGIYPIASFLNTIVTAGWFSMQGWPLVYGMFATAMTILLLMIGTNWTESYLYSGYYINRGIHTYLCL
GLFDKITYYPHFPIKDSDSTLGLPNNSGTEHLFTLHVGALAVMTFPLIFHFAFFRNLTAKDVSFGGWIWE
LIVISLFLALVGGLKNPVSRLIAYAFLFYWEPKIHLPTNLPDAPMHNDPDGLMDPSLLALLLLLLILILL
executor >  local (2)
[ac/3e7150] process > splitSequences [100%] 1 of 1 ✔
[c4/de9f8e] process > reverse        [100%] 1 of 1 ✔
Completed at: 28-Jun-2019 11:21:10
Duration    : 1.1s
CPU hours   : (a few seconds)
Succeeded   : 2

FASTA format - Wikipedia
따라서 다음 배열을 data/sample2.fa로 저장

>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
DIDGDGQVNYEEFVQMMTAK*

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY

입력 파일 변경하기

$ ./nextflow example1.nf --in=data/sample2.fa

work 아래에 데이터가 나와 있습니다.

seq-1
seq-2