[Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv

[ctuni]

Description of the bug

When trying to run the pipeline, and passing the samplesheet from inside either a config file or a params file, the following error appears:

The command used to run the pipeline is:
nextflow run nf-core/differentialabundance -c file.config -params-file params.yml

I'm not explicitly using the -profile flag because I have them defined in .nextflow/.config, but they would be -profile docker,awsbatch.

ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (1)'

Caused by:
  Not a valid path value: 'samplesheet.csv'

The file samplesheet.csv is in the same directory as the param and config files and also the same directory where I'm launching the pipeline.

The contents of file.config are:

fusion.enabled = true
wave.enabled = true

process {
    scratch = true
    cpus   = { 1 * task.attempt }
    memory = { 1.GB * task.attempt}
    time   = {10.m  * task.attempt}

    errorStrategy = 'retry'
    maxRetries    = 5
    maxErrors     = '-1'
}

workDir = 's3://scratch-bucket/nextflow-workdir/'

Passing the input in the config file as params { input = 'samplesheet.csv'} does not work either.

The contents of params.yml are:

input: samplesheet.csv
outdir: 's3://data-bucket/nf-core_diff-abund_2023-05-08'
matrix: 's3://data-bucket/star_salmon/salmon.merged.gene_counts.tsv'
gtf: 's3://data-bucket/sorted.gtf'
contrasts: contrasts.csv
observations_id_col: 'sample'
observations_name_col: 'sample'
tracedir: './pipeline_info'

I have tried with adding single and double quotes around the file name and the error is the same. When adding the full path of the samplesheet, the error is the following:

ERROR ~ Unable to read script: '/mnt/efs/home/ctuni/.nextflow/assets/nf-core/differentialabundance/./workflows/differentialabundance.nf' -- cause: /mtn/efs/home/ctuni/diff_ab/FL-LC_samplesheet.csv

 -- Check script '/mnt/efs/home/ctuni/.nextflow/assets/nf-core/differentialabundance/main.nf' at line: 37 or see '.nextflow.log' file for more details

Finally, simply running nextflow run nf-core/differentialabundance -c file.config -params-file params.yml --input samplesheet.csv also gives the first error.

A thing I did to solve this is to first upload the samplesheet to S3 and pass it on the params file like: input: 's3://path-to-the-samplesheet.csv'. This works.

Also, user Brad Olson mentioned that they encountered the same issue and rolling back to version 1.0.1 solved the issue for them. I have not tried this.

Command used and terminal output

No response

Relevant files

No response

System information

Nextflow version 23.04.1
In AWSbatch using Docker
Amazon Linux v3
Version of nf-core/differentialabundance: 1.2.0