I want to pass the input file through an argument unfortunately not with params-file, reason being unable to use the params-file in the nftower dashboard under Pipeline parameters field which is equivalent to params-file option allowing to paste the json/yaml file in the field but it has a charcters limitation to give large number of samples list. To overcome this I need to give the input file with an arg like. insput_list: s3://my-bucket/params.yaml
Nextflow - How to pass the yml format input file from an argument to channel as a list
How to pass the yml format input file from an argument to a channel samples as a list? Appreciate if any nextflow function or simple solution to make the channel samples works with --input_list s3://my-bucket/params.yml instead of -params-file s3://my-bucket/params.yml
The given below channel samples code works with -params-file s3://my-bucket/params.yml but that's not I'm looking.
$ nextflow run main.nf \ -config nextflow.config \ --input_list s3://my-bucket/params.yml \ --publish_dir ./output
--input_list s3://my-bucket/params.yml
samples:
-
biosample_id: WGS001
bam: WGS001.bam
-
biosample_id: WGS0002
bam: NWGS0002.bam
workflow
Channel
.fromList( params.samples )
.ifEmpty { ['biosample_id': params.biosample_id, 'bam': params.bam] }
.set { samples }
Channel
samples.branch { rec ->
....
Channel
samples.map { it.biosample_id }
....
3 answers
I don't think there is a native NF operator to read YAML:
Nevertheless, nextflow itself contains a java library parsing yaml. org.yaml.snakeyaml.Yaml
So you can try:
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Pierre Lindenbaum
I'd recommend to use a csv file to give out input file instead. This is what we do most of the time in nf-core nowadays.
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Maxime Garcia
How come undocumented? https://www.nextflow.io/docs/latest/cli.html?highlight=params%20file
There are even examples over there.
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Marcel Ribeiro-Dantas •
This works well...
import groovy.yaml.YamlSlurper
params.inputs_list = "inputs.yaml"
workflow {
inputs = new YamlSlurper().parse(file(params.inputs_list))
Channel
.fromList(inputs['samples'])
.ifEmpty { ['biosample_id': params.biosample_id, 'aln': params.aln] }
.set { samples }
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