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}
"""
}