Nextflow manipulate variables between processes

Question

I am redesigning a workflow, basically it starts off with a process which spawns multiple other processes. Initially I had the variables before starting my workflow and so I made a tuple of these variables and then passed it as input to a process. The process gets each value, and spawns a process for each value in the tuple.

However in my new architecture I get the 'tuple' in my processA. And processB then needs to take each value as input, and spawn one process per input.

My tuple looks like: {"002--002": some_params, "004--004": some_params, etc.}

I currently have these values as a list in Python: ['052--052', '054--054', '055--055', '059--059', '060--060', '066--066']

I was wondering how can I parse this Python list, to keep passing one argument and spawn multiple processes?

ProcessA also creates files such as somefile_052--052.someextension - and I basically want to pass the correct variable with the correct file.

Any help would be greatly appreciated.

Here is some code:

This is the files that I need to manipulate. I need to send all files with the same code, alongside the variable.

> ls
out.barcoded.subreads.bam             out.subreads.060--060.bam.pbi         out.subreads.090--090.subreadset.xml  out.subreads.149--149.bam             out.subreads.192--192.bam.pbi         out.subreads.249--249.subreadset.xml  out.subreads.285--285.bam             out.subreads.321--321.bam.pbi         out.subreads.479--479.subreadset.xml
out.barcoded.subreads.bam.pbi         out.subreads.060--060.subreadset.xml  out.subreads.091--091.bam             out.subreads.149--149.bam.pbi         out.subreads.192--192.subreadset.xml  out.subreads.252--252.bam             out.subreads.285--285.bam.pbi         out.subreads.321--321.subreadset.xml  out.subreads.482--482.bam
out.barcoded.subreads.lima.counts     out.subreads.066--066.bam             out.subreads.091--091.bam.pbi         out.subreads.149--149.subreadset.xml  out.subreads.227--227.bam             out.subreads.252--252.bam.pbi         out.subreads.285--285.subreadset.xml  out.subreads.454--454.bam             out.subreads.482--482.bam.pbi
out.barcoded.subreads.lima.guess      out.subreads.066--066.bam.pbi         out.subreads.091--091.subreadset.xml  out.subreads.172--172.bam             out.subreads.227--227.bam.pbi         out.subreads.252--252.subreadset.xml  out.subreads.303--303.bam             out.subreads.454--454.bam.pbi         out.subreads.482--482.subreadset.xml
out.barcoded.subreads.lima.report     out.subreads.066--066.subreadset.xml  out.subreads.107--107.bam             out.subreads.172--172.bam.pbi         out.subreads.227--227.subreadset.xml  out.subreads.259--259.bam             out.subreads.303--303.bam.pbi         out.subreads.454--454.subreadset.xml  out.subreads.489--489.bam
out.barcoded.subreads.lima.summary    out.subreads.071--071.bam             out.subreads.107--107.bam.pbi         out.subreads.172--172.subreadset.xml  out.subreads.233--233.bam             out.subreads.259--259.bam.pbi         out.subreads.303--303.subreadset.xml  out.subreads.464--464.bam             out.subreads.489--489.bam.pbi
out.barcoded.subreads.subreadset.xml  out.subreads.071--071.bam.pbi         out.subreads.107--107.subreadset.xml  out.subreads.175--175.bam             out.subreads.233--233.bam.pbi         out.subreads.259--259.subreadset.xml  out.subreads.307--307.bam             out.subreads.464--464.bam.pbi         out.subreads.489--489.subreadset.xml
out.subreads.052--052.bam             out.subreads.071--071.subreadset.xml  out.subreads.112--112.bam             out.subreads.175--175.bam.pbi         out.subreads.233--233.subreadset.xml  out.subreads.261--261.bam             out.subreads.307--307.bam.pbi         out.subreads.464--464.subreadset.xml  out.subreads.494--494.bam
out.subreads.052--052.bam.pbi         out.subreads.082--082.bam             out.subreads.112--112.bam.pbi         out.subreads.175--175.subreadset.xml  out.subreads.235--235.bam             out.subreads.261--261.bam.pbi         out.subreads.307--307.subreadset.xml  out.subreads.468--468.bam             out.subreads.494--494.bam.pbi
out.subreads.052--052.subreadset.xml  out.subreads.082--082.bam.pbi         out.subreads.112--112.subreadset.xml  out.subreads.185--185.bam             out.subreads.235--235.bam.pbi         out.subreads.261--261.subreadset.xml  out.subreads.313--313.bam             out.subreads.468--468.bam.pbi         out.subreads.494--494.subreadset.xml
out.subreads.054--054.bam.pbi         out.subreads.082--082.subreadset.xml  out.subreads.113--113.bam             out.subreads.185--185.bam.pbi         out.subreads.235--235.subreadset.xml  out.subreads.264--264.bam             out.subreads.313--313.bam.pbi         out.subreads.468--468.subreadset.xml  out.subreads.bam
out.subreads.054--054.subreadset.xml  out.subreads.085--085.bam             out.subreads.113--113.bam.pbi         out.subreads.185--185.subreadset.xml  out.subreads.241--241.bam             out.subreads.264--264.bam.pbi         out.subreads.313--313.subreadset.xml  out.subreads.471--471.bam             out.subreads.bam.pbi
out.subreads.055--055.bam             out.subreads.085--085.bam.pbi         out.subreads.113--113.subreadset.xml  out.subreads.187--187.bam             out.subreads.241--241.bam.pbi         out.subreads.264--264.subreadset.xml  out.subreads.316--316.bam             out.subreads.471--471.bam.pbi         out.subreads.json
out.subreads.055--055.bam.pbi         out.subreads.085--085.subreadset.xml  out.subreads.125--125.bam             out.subreads.187--187.bam.pbi         out.subreads.241--241.subreadset.xml  out.subreads.265--265.bam             out.subreads.316--316.bam.pbi         out.subreads.471--471.subreadset.xml  out.subreads.lima.counts
out.subreads.055--055.subreadset.xml  out.subreads.088--088.bam             out.subreads.125--125.bam.pbi         out.subreads.187--187.subreadset.xml  out.subreads.245--245.bam             out.subreads.265--265.bam.pbi         out.subreads.316--316.subreadset.xml  out.subreads.473--473.bam             out.subreads.lima.guess
out.subreads.059--059.bam             out.subreads.088--088.bam.pbi         out.subreads.125--125.subreadset.xml  out.subreads.188--188.bam             out.subreads.245--245.bam.pbi         out.subreads.265--265.subreadset.xml  out.subreads.317--317.bam             out.subreads.473--473.bam.pbi         out.subreads.lima.report
out.subreads.059--059.bam.pbi         out.subreads.088--088.subreadset.xml  out.subreads.143--143.bam             out.subreads.188--188.bam.pbi         out.subreads.245--245.subreadset.xml  out.subreads.273--273.bam             out.subreads.317--317.bam.pbi         out.subreads.473--473.subreadset.xml  out.subreads.lima.summary
out.subreads.059--059.subreadset.xml  out.subreads.090--090.bam             out.subreads.143--143.bam.pbi         out.subreads.188--188.subreadset.xml  out.subreads.249--249.bam             out.subreads.273--273.bam.pbi         out.subreads.317--317.subreadset.xml  out.subreads.479--479.bam             out.subreads.subreadset.xml
out.subreads.060--060.bam             out.subreads.090--090.bam.pbi         out.subreads.143--143.subreadset.xml  out.subreads.192--192.bam             out.subreads.249--249.bam.pbi         out.subreads.273--273.subreadset.xml  out.subreads.321--321.bam             out.subreads.479--479.bam.pbi

So I would like to send these files, and this variable: 059--059

out.subreads.059--059.bam
out.subreads.059--059.bam.pbi
out.subreads.059--059.subreadset.xml

Currently my code in the workflow is:

process procA{
    input:
    file bc_fasta from bc_fasta_chan

    output:
    set file("$analysis_config.cell/bam/out.subreads.*"), val("$analysis_config.cell/bam/out.subreads.*") into lima_out

    script:
    ```
    // run script to generate the above generated files
    ```
}

process procB{
    input:
    set file(bc_bam_file), val(bc_name) from lima_out.flatten()

    script:
    """
    ls
    echo ${bc_bam_file}
    """
}

user_751863 · Answer

The trick is to be able to extract somehow the grouping variable from the filenames, and then call groupTuple. I've just used a simple regex to get this variable, but you could implement something more sophisticated if necessary:

lima_out = Channel.fromPath( './files/out.subreads.*', relative: true )

subreads_pattern = ~/^out\.subreads\.(\d{3}--\d{3})\..*/

lima_out
    .flatten()
    .filter { it.name =~ subreads_pattern }
    .map { tuple( (it.name =~ subreads_pattern)[0][1], it ) }
    .groupTuple(size: 3, sort: true)
    .view()

Results:

[489--489, [out.subreads.489--489.bam, out.subreads.489--489.bam.pbi, out.subreads.489--489.subreadset.xml]]
[316--316, [out.subreads.316--316.bam, out.subreads.316--316.bam.pbi, out.subreads.316--316.subreadset.xml]]
...

Here's an example of how I would input these values into a process. My preference for handling companion files (in this case, we have files with the '.bam.pbi' extension) is to keep these alongside the BAM files. I just use a tuple for this. By calling first() on our tuple, we can get the BAM. This is just my preference though. You could have a separate file/path variable in your input tuple for the pbi companion file but you probably won't need to reference it in your script block.

lima_out = Channel.fromPath( './files/out.subreads.*', relative: true )

subreads_pattern = ~/^out\.subreads\.(\d{3}--\d{3})\..*/

lima_out
    .flatten()
    .filter { it.name =~ subreads_pattern }
    .map { tuple( (it.name =~ subreads_pattern)[0][1], it ) }
    .groupTuple(size: 3, sort: true)
    .map { group_name, files -> tuple( group_name, files[2], files[0..1] ) }
    .set { subreads_ch }

process next_process {

    input:
    tuple val(group), path(subreadset), path(indexed_subreads) from subreads_ch

    """
    echo "subreadset XML: ${subreadset}"
    echo "subreads BAM: ${indexed_subreads.first()}"
    """
}

Nextflow manipulate variables between processes

1 Answers