如何打造文件的价值通道？

Question

如何将文件输入添加到多个并行进程？

我想做这样的事情：

proteins = Channel.fromPath( '/some/path/*.fa' )
executions = Channel.from(1, 2, 3, 4)

process blastThemAll {
  input:
  val num from executions
  file query_file from proteins

  "blastp -query ${query_file} -db nr"

}

我想要 4 个进程，每个进程都可以访问蛋白质通道中的所有文件。基本上，我希望蛋白质通道成为包含文件列表的价值通道。

我找不到怎么做...

Answer 1

您可以使用 collect 运算符，它将通道发出的所有项目收集到列表中，并且 return 生成的对象作为唯一发射。

A value channel is created using the value factory method or by operators returning a single value, such us first, last, collect, count, min, max, reduce, sum.

例如：

proteins = Channel.fromPath( '/some/path/*.fa' ).collect()
executions = Channel.from(1, 2, 3, 4)

process blastThemAll {

  tag { "job ${num}" }

  input:
  val num from executions
  path query_file from proteins

  """
  find . -name '*.fa'
  """
}

和运行与：

nextflow run -ansi-log false test.nf

结果：

N E X T F L O W  ~  version 21.04.3
Launching `test.nf` [gloomy_mclean] - revision: 53ee46a154
[c9/6da993] Submitted process > blastThemAll (job 4)
[0e/24cc9b] Submitted process > blastThemAll (job 1)
[43/c500eb] Submitted process > blastThemAll (job 2)
[6b/d75ce4] Submitted process > blastThemAll (job 3)

如何打造文件的价值通道？

How to create a value channel of files?

nextflow