Hi,
I have a minimal pipeline, with an apptainer.
Parquet in, parquet out.
The apptainer step is calculating the right stuff, and spits it out to results.
So it seems nothing is wrong with the container itself.
However, the collectFile is not working.
Does this work with apptainer?
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
include { CALCULATE_BIOPYTHON_FEATURES } from './modules/biopython'
include { CHECKSUM } from './modules/checksum'
// Pipeline parameters with defaults
params.input = "$projectDir/total_dataset.parquet"
params.output = 'output.parquet'
workflow{
Channel.fromPath(params.input, checkIfExists: true) \
| CHECKSUM \
| CALCULATE_BIOPYTHON_FEATURES \
| collectFile(name: params.output)
}
process CALCULATE_BIOPYTHON_FEATURES {
container 'containers/biopython.sif'
publishDir 'results', mode: 'copy'
input:
path preprocessed_file
output:
path "biopython.parquet", emit: biopython_features
script:
"""
python /workdir/biopython.py --input_path ${preprocessed_file} --output_path biopython.parquet
"""
}