Trouble running with " --input '*_R{1,2}.fastq.gz' "

[LiamPorter6]

If I have a directory of multiple paired-end (R1/R2) .fastq.gz files how would I format the code? --input '*_R{1,2}.fastq.gz' returns errors.
Even when I do one sample : --input 'sample1_R{1,2}.fastq.gz' , I get an error: ERROR ~ Input length = 1
It seems like it only reads the firs fastq.gz in the directory
When I do: --input samplesheet.csv , it runs correctly but using **fastq.gz or R1.fastq.gz,R2.fastq.gz would be faster that creating a csv file in the correct format.
Could you make an example command all fastq.gz paired-end files in current directory as the input:
nextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '_R{1,2}.fastq.gz' --outdir

[jfy133]

Hello @LiamPorter6

Supplying reads directly via --input is no longer supported since version 3.3.0.

Code wise, handling both methods was difficult to maintain, and with recent additions such as assembly input, and upcoming long-read only support we need more metadata about each assembly than can be supported by command line flags.

You will have to use samplesheets for now - however you could probably make a little script to auto-generate a samplesheet for you from a pattern as used to be supported.

[LiamPorter6]

thank you!