[New Feature Request] - Allow AWS S3 path for the CREATE_SRA_SAMPLESHEET function

[vitu1]

When running Phoenix on AWS Batch using the --input_sra flag, the pipeline will fail on the SAMPLESHEET_CHECK step. It looks like the sample sheet generated by CREATE_SRA_SAMPLESHEET uses the file system path of an initialized instance instead of the S3 path where the file is deposited. This causes the downstream process SAMPLESHEET_CHECK to fail when looking for the downloaded FASTQ file

Allowing CREATE_SRA_SAMPLESHEET to use an S3 bucket path defined in the param '--outdir' may help resolve this issue

[NoForkJustCommit]

Can you provide the .nextflow.log file (if you don't want to post it here you can email to HAISeq.cdc.gov). I think there are some updates to the nextflow that improve its interaction with cloud platforms. What version of Nextflow are you running?

[vitu1]

I am using Nextflow version 24.10.3

Here's the command I used:

nextflow run cdcgov/phoenix
-profile phoenix_test
-bucket-dir s3://nextflow-workdir/phoenix_test_2025-02-10
-r v2.1.1
-entry SRA
--input_sra s3://test-environment/input/test_phoenix_2025-02-10/test_accessions.csv
--kraken2db s3://error/before/this/step/
--outdir s3://test-environment/output/test_phoenix_2025-02-10/

I've attached the relevant files

nextflow.log
nf_config.txt
test_accessions.csv
sra_samplesheet.csv