it's not my pipeline, so I don't have too much control over the basic logic of it all, just trying to implement support for multiple input data sets (right now it assumes that there is only one sample)
it used to be multiple arguments under "input:" with an added ".ifEmpty('')" - but that seems difficult to do now
well the empty channel needs to emit something at least, then one could try to verify each element to see if it is an actual file or just a placeholder , like "''" or NULL
problem is that this will require much more substantial changes, since we want to join/mix based on a key - so it would have to be [ some_key, NULL ] or something along those lines :D I think the whole pipeline needs to be set up in a different way.... maybe have the reporting step be like MultiQC so that it automatically detects which outputs are present or whatever
and just skip the need for dummy values...
I've experimented a bit .... with a setup like the following, you could perhaps stick some intelligence in the script section to detect what it has?
a = Channel.from(['a', 1], ['b', 2])
b = Channel.from(['a', 3], ['b', 4])
c = Channel.from(['a', 5], ['b', 6])
d = Channel.empty()
a.mix(b).mix(c).mix(d).groupTuple().view().set { ch }
process bar {
input: set val(a), val(b) from ch
echo true
shell:
'''
echo "one value !{a} other values !{b}"
'''
}
any ideas why a function from a package in R would not be found when run in singularity via nextflow? e.g. could not find function "sumCountsAcrossCells"
and even calling the function with scater::sumCountsAcrossCells gives "Error: 'sumCountsAcrossCells' is not an exported object from 'namespace:scater'
and even calling the function with scater::sumCountsAcrossCells gives "Error: 'sumCountsAcrossCells' is not an exported object from 'namespace:scater'
I am trying to use a parameter from
params inside a .map call. Is that possible?
This is what I want to do
bed_split_ch = bed_ch
.map{it -> tuple(it[0],it[1].splitText(by: 2, file: true))}and it works. I would like to use params.splitBed instead of 2.
hey I also posted this in the Google groups, but I am trying to come up with methods to implement unit testing and CI for Nextflow pipelines. I got as far as doing
unittest in Python, but I am not sure what exactly I should be testing. Any suggestions? My work so far is here: https://github.com/stevekm/nextflow-ci
also helpful I guess in that I also started a super basic module to run Nextflow from Python, its in there under
nextflow.py, mostly just a CLI wrapper with ENV variables thrown in
Hi all, I have a process that should be performed only when a parameter is a certain value. So I use the "when" condition. The problem I have is that the script is complaining for the absence of the input channel in that process even if the condition is not met... If I make an empty channel then it hangs without doing nothing... is this the normal behaviour?
How can I convert a channel object into a normal Groovy object? For example, I have a process that emits a directory, and I need this directory as a string to do some regex on the filenames in the folder. See example below.
[Process that emits a folder to "process1_ch"]
// Get the path in process1_ch
path = ?????????
// Do something with the path
new_ch = Channel.fromPath(path + '*somefilepatternmatching')
.map { do something with the data }
[Process that uses "new_ch"]
I run in to these kinds of issues all the time, and end up using some workaround. Surely there's some way to do this.
new_ch
To me, an obvious solution seems to be
toList(https://www.nextflow.io/docs/latest/operator.html#tolist), but that doesn't seem to do the job
Here's the actual code:
// Get the sample names from the files in the output FASTQ folder by regex.
sample_names_ch = Channel.fromPath(bcl2fastq_outdir + '/*.fastq.gz')
.map { it.toString() }
.map { it.replaceAll(/\/.*\//, "") } // Remove everything leading up to the sample name.
.map { it.replaceAll(/_.*/, "") } // Remove everything after the sample name.
.unique()
from filenames
Trying to get sample names from file names