Hi, I realized, that it seems like bool inputs that are provided via a samplesheet are converted to Strings. What is the best way to avoid this?

Not sure how this deals with the things that come in via

.splitCsv

hmm, not sure. Do you know, @Nicolas Vannieuwkerke ?

How are you reading the samplesheet? .splitCsv does not have any type casting AFAIK so CSV and TSV samplesheet values will always be String values.

Hm, that's good to know, I will need to update a bunch of stuff. Is there a csv reader with typecasting?

You can use #C056RQB10LU which contains a

samplesheetToList

function that validates and converts a samplesheet to a list

Is there also

samplesheetToMap

?

Nope, but you could set all values as meta values and then it will create a list of maps, one map per samplesheet entry

Hm, I am not sure if that will work for me, especially because of:

It is the order of fields in the sample sheet JSON schema which defines the order of items in the channel returned by

samplesheetToList()

, not the order of fields in the sample sheet file.

That's not the case if you make all values meta values

Ah, I get it now

I'm planning on implementing a new

samplesheetToRecords

function to support record types in the future so that might be useful for you then

Thanks a lot, that is probably much better than typecasting everything manually

Glad I could help 😛 let me know if something is not working as expected

I have never used nf-schema, in my case my samplesheet schema is almost fully identical with my params; can I just use

nextflow_schema.json

as a basis, and add the meta fields?

That should be possible, although I've never tried it myself

When I try this, for example:

"shortread_F": {
                "type": "string",
                "description": "Path to forward short reads",
                "meta": ["shortread_F"]
            }

and then later try:

file(meta.shortread_F)

I get:

Unknown method invocation `getFileSystem` on ArrayList type

Is there an easy way to solve that?

You can let nf-schema convert that to a file object automatically using

"format": "file-path"

. This error usually means that the file has not been given via the samplesheet and that it defaults to

[]

which is the default value if something is missing. It would also help if you could show me the output of the function

ah, I will try file-path

You can also change the default value with

"default": <default-value>

It would also help if you could show me the output of the function

You mean the function that fails?

if (!file(row.shortread_F).exists()) {
        exit(1, "ERROR: shortread_F fastq file does not exist!\n${row.shortread_F}")
    }

no the output of

samplesheetToList

sorry I should have been more clear

It looks like this:

Parsed samplesheet: [meta:[id:[null], group:[null], ontreads:[[]], hifireads:[[]], strategy:[single], assembler:[hifiasm], assembler_ont:[[]], assembler_hifi:[hifiasm], assembly_scaffolding_order:[ont_on_hifi], assembler_ont_args:[[]], assembler_h
ifi_args:[[]], hifiasm_args:[[]], flye_args:[[]], polish:[null], ont_collect:[[]], ont_adapters:[[]], ont_fastplong_args:[[]], jellyfish:[[]], jellyfish_k:[null], jellyfish_size:[200M], hifi_adapters:[[]], hifi_fastplong_args:[[]], medaka_model:[[
]], scaffold_longstitch:[[]], scaffold_links:[[]], scaffold_ragtag:[[]], scaffold_hic:[false], use_ref:[[]], hic_aligner:[bwa-mem2], hic_F:[[]], hic_R:[null], hic_trim:[[]], genome_size:[[]], ref_fasta:[[]], ref_gff:[[]], flye_mode:[--nano-hq], as
sembly:[[]], ref_map_bam:[[]], assembly_map_bam:[[]], qc_reads:ont, qc_reads_path:[[]], quast:[[]], busco:[[]], busco_lineage:[auto_euk], busco_db:[[]], meryl_k:[21], merqury:[false], lift_annotations:[false], shortread_F:[[]], shortread_R:[[]], p
aired:[[]], use_short_reads:[[]], shortread_trim:[[]]]]

I think I need to default to

null

, or anything else that will evaluate to false with

?

not in the schema but you can easily do this in pipeline code like this:

meta.key = meta.get("key", params.paramname}

not sure if I get what you mean, or if that is meaningfully different from what I am already doing wich is basically:

.map{ it -> [meta:[key: it.meta.key ?: params.key ]]}

does that work? 😅 but yeah it should be very similar

it used to work, but I am bit worried that with keys receiving defaults from nf-schema it will no longer work

[]

is also considered

false

in groovy so that's fine

hm, not so sure

But if I get it right you have a map containing one value which is the meta, which itself is a map of values?

everything that is

[[]]

in the dumped output above should have a value

It's weird that these values are lists of lists though 🤔 could you send me your full schema?

this is what I did so far github.com/nf-core/genomeassembler/blob/…/main.nf#…

your schema looks fine 😛

Great 😄

Could you also point me to some code with nf-schema?

it is the same as before except that it starts:

ch_samplesheet = channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))

That should be fine, let me know if you have a PR I can try some things then 😛

I can create a PR if you would like to do some things 🙂

That would be wonderful 😛

okay give me some time 😛 I'll see if I can reproduce it, were you just using the test profile for this?

What I want to do is simple: If something comes in via the samplesheet, give it the samplesheet value in

meta.key

, if it does not come via the samplesheet give it the value of

params.key

Is the meta key name always the same as the parameter? Because that could be simplified 😛

yes, it is always the same, because otherwise I would get completely lost lol

Perfect!

There is one exception: github.com/nf-core/genomeassembler/blob/…/main.nf#… but I can probably find a way to handle that

Okay so your code seems to make the lists in lists somehow because the output of

samplesheetToList

is correct, I'll dig a bit deeper 😛

Its nice that we reach the same conclusion

I see the problem,

samplesheetToList

creates a list with one value (the meta map) so your

it

is actually

List[meta]

instead of just

meta

. You need to fetch it from it like that.

amazing

You're welcome! You can still apply some manual code on the output of the

collectEntries

method 😉

Always happy to apply some manual code

Hack away 😉