Configure S3 for units.tsv

[nttg8100]

I upload the input file to the remote S3 bucket. I have this units.tsv as below and correctly used put the S3 credential in the config file. However, it seems that the function to retrieve the fq file can not recognize it as nextflow does. Is that snakemake does not support this feature or I'm doing something wrong ?

sample_name	unit_name	fq1	fq2	sra	fastp_adapters	fastp_extra	strandedness
A1	1	s3://genomics/ngs-test-data/reads/a.scerevisiae.1.fq	s3://genomics/ngs-test-data/reads/a.scerevisiae.2.fq		--adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA		yes
B1	1	s3://genomics/ngs-test-data/reads/c.scerevisiae.1.fq	s3://genomics/ngs-test-data/reads/c.scerevisiae.2.fq		--adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA		none
A2	1	s3://genomics/ngs-test-data/reads/c.scerevisiae.1.fq	s3://genomics/ngs-test-data/reads/c.scerevisiae.2.fq		--adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA		none
B2	1	s3://genomics/ngs-test-data/reads/b.scerevisiae.1.fq	s3://genomics/ngs-test-data/reads/b.scerevisiae.2.fq		--adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA		reverse

[dlaehnemann]

Are you already using the s3 storage plugin? If not, have a look here:
https://snakemake.github.io/snakemake-plugin-catalog/plugins/storage/s3.html

[nttg8100]

I already install the plugin, but it shows me that it works with a single file as input instead of samplesheet.

[nttg8100]

I think it does not support samplesheet, I uploaded and used the gtf file from s3, it ran successfully. If snakemake does not support, I will close it

[dlaehnemann]

From what I can see, you are not using a profile, right? But I think you need to configure things like the S3 endpoint:
https://snakemake.github.io/snakemake-plugin-catalog/plugins/storage/s3.html#within-the-workflow

But I also haven't used S3 myself, yet. So I'm not absolutely sure how the setup should look.