Unable to parse config file

Question

[JieQY]

I'm currently trying to automate genome assembly (fastq files) using nf-core/genomeassembler, but I'm having trouble downloading and running the project. I currently think that my nextflow and nf-core have been installed successfully (using conda). Nextflow:

nextflow run hello

Output:

bash: /users/jieqyan/miniconda3/lib/libtinfo.so.6: no version information available (required by bash)

N E X T F L O W   ~  version 24.10.5
Launching `https://github.com/nextflow-io/hello` [prickly_kilby] DSL2 - revision: afff16a9b4 [master]
executor >  local (4)
[a7/359fd7] sayHello (4) | 4 of 4
Bonjour world!
Ciao world!
Hello world!
Hola world!

nf-core: Running the command:

nf-core pipelines list

is also fine.

However, when I try to download the nf-core/genomeassembler data from GitHub via:

nextflow run nf-core/genomeassembler

the following error occurs:

bash: /users/jieqyan/miniconda3/lib/libtinfo.so.6: no version information available (required by bash)

N E X T F L O W   ~  version 24.10.5
ERROR ~ Unable to parse config file: '/users/jieqyan/.nextflow/assets/nf-core/genomeassembler/nextflow.config'

Cannot read config file include: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config

-- Check '.nextflow.log' file for details

I tried to download the configuration file directly and put it in the folder, but the same error occurred.

When running:

nextflow pull nf-core/genomeassembler -revision 1.0.1

I get:

bash: /users/jieqyan/miniconda3/lib/libtinfo.so.6: no version information available (required by bash)
Checking nf-core/genomeassembler ...
Unexpected end of file from server

This may be caused by the server network, but I don't know how to solve it. I would be grateful if you could provide me with any advice!

[ATpoint]

I cannot reproduce the problem. The pull command works for me, and your error with nextflow run is probably expected because you have not configured anything (at least you don't mention to have done so, so it doesn't know where to look for input files etc? See https://nf-co.re/genomeassembler/dev/docs/usage/ on how to get going.

This may be caused by the server network, but I don't know how to solve it.

This you have to sort out locally with the server admin.

Note that you don't need conda to install nextflow, check its documentation, there is a simple one-liner to create the binary. I would be concerned about this lib error you see all the time. Consider removing this conda env and start via Getting Started at https://www.nextflow.io/

[Phil Ewels]

Agreed, I also just tested it (with the following to try to mimic your setup exactly):

NXF_VER=24.10.5 nextflow run nf-core/genomeassembler -r 1.0.1

I get a bunch of output, ending with this (as expected):

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* Missing required parameter(s): input, outdir

I suspect that this is a network issue, but it's a bit of a strange one if those other commands are working..