CODEWITHSUNDEEP
nextflow
raygozag
raygozag

Reputation: 218

Nextflow channel only processing first tuple in channel

i'm loading single end files into an align process in nextflow. I view the channel and it shows both files (there are only two files in my exmple):

Channel.fromFilePairs(params.fastqfiles,size: 1,checkIfExists: true ).set{file_list_ch}
file_list_ch.view()

[193fin, [193fin.fastq.gz]]

[829fin, [829fin.fastq.gz]]

But then when run a process with this channel, it only uses the first one and

[1a/11f063] process > INDEX (1) [100%] 1 of 1 ✔
[e7/89e2be] process > ALIGN (1) [100%] 1 of 1 ✔

part of the process is as follows:

ALIGN(index_ch,file_list_ch)



process ALIGN{

     
    


    input:
        path index, stageAs: "bowtie_index/*"
        tuple val(sample_id), path(reads)

I have the example of the nf-core workshop and it's identical except it is single ended, but it still just runs one process.

how can i make it run all the processes?

Thanks

Upvotes: 1

Views: 816

Answers (1)

Steve
Steve

Reputation: 54502

Issues like this almost always involve the use of multiple input channels:

When two or more channels are declared as process inputs, the process waits until there is a complete input configuration, i.e. until it receives a value from each input channel. When this condition is satisfied, the process consumes a value from each channel and launches a new task, repeating this logic until one or more channels are empty.

You didn't show how index_ch was created, but I suspect it is actually a queue channel. What you want instead is a value channel:

A different semantic is applied when using a value channel. This kind of channel is created by the Channel.value factory method or implicitly when a process is invoked with an argument that is not a channel. By definition, a value channel is bound to a single value and it can be read an unlimited number of times without consuming its content. Therefore, when mixing a value channel with one or more (queue) channels, it does not affect the process termination because the underlying value is applied repeatedly.

Upvotes: 0

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