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2 votes

Where do I find which PGS Calculator version I am using?

Since you are running via singularity you can find out the version you are using from the container, defined in modules.config for this pipeline (https://github.com/PGScatalog/pgsc_calc/blob/main/conf%...
Niklas's user avatar
  • 126
2 votes
Accepted

Nextflow: Properly chaining process outputs

This is a result of nextflow channel types, queue- and value-channels. Nextflow will make fifo combinations of your channels to run bwa_align until either or both ...
Pallie's user avatar
  • 706
2 votes
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Export multiple variables from shell script into a Nextflow output channel

I am not sure if i get what you mean by encapsulate, you can give your tuple a name using emit? ...
Niklas's user avatar
  • 126
2 votes
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Error output in nextflow pipeline using fasterq-dump

Each nextflow process looks in its working directory for the files listed in output: . In your script: you already direct the ...
Pallie's user avatar
  • 706
2 votes
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nextflow: merge lane files from samples forward and reverse read

I think you are on the right track using groupTuple(sort: true). Another way to get what you want would be to instead parse the ...
Steve's user avatar
  • 3,109
2 votes
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nextflow: unable to find index

I am reluctant to go through this wall of code, but generally it is advisable to always keep bam files and its index in a tuple so the index is staged with its bam file. For example a process that ...
ATpoint's user avatar
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2 votes
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nextflow: tumor normal sample - how to make code organic

I think you have a design problem here. A better way would be perform this operation in your workflow block. This would allow you to feed in the tumor and normal BAMs (and avoid accessing files ...
Steve's user avatar
  • 3,109
1 vote

How fo force nextflow to repeat a process until all values in a particular channels are used up BUT a single value from another channel is needed

Use a value channel: exampleChannel_onething = Channel.value(1) On existing channels, you can use https://www.nextflow.io/docs/latest/operator.html#first (or ...
Rolf's user avatar
  • 111
1 vote
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Nextflow - Missing value declared as output parameter - output variable defined in script

You would like to use the sample_name variable outside the script block, but the def keyword defines a variable locally. All you'...
Steve's user avatar
  • 3,109

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