Possible error when checking awsbatch profile and workflow.tracedir

[lpantano]

I came with this error when doing

nextflow run nf-core/rnaseq -profile awsbatch,test, if you add a prinln workflow.profile, you will see it it awsbatch,test that is not equal to the line that is checking for that in main.nf:

if (workflow.profile == 'awsbatch') {

This command will give an error, but it is a nexflow error saying:

When using `awsbatch` executor a S3 bucket must be provided as working directory either using -bucket-dir or -work-dir command line option

And not the expecting one from main.nf:

Outdir not on S3 - specify S3 Bucket to run on AWSBatch!

or even:

Specify a local tracedir or run without trace! S3 cannot be used for tracefiles

Besides, if you do this, you will see this error:

nextflow run nf-core/rnaseq -profile awsbatch --awsqueue default-6edd1010-f59e-11e9-ab0a-12dffdf25cac  --awsregion us-east-1 -w s3://egenesis-data-processed/nextflowdataegenesis/lpantano_devel/test/work0611 --outdir s3://egenesis-data-processed/nextflowdataegenesis/lpantano_devel/test/out0611 --reads 'https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/SRR4238351_subsamp.fastq.gz' --fasta 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa' --gtf 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf'
N E X T F L O W  ~  version 19.07.0
Launching `nf-core/rnaseq` [extravagant_watson] - revision: 3b6df9bd10 [master]
Unexpected error [StackOverflowError]

Due to this line:

  if (workflow.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."

if you do log.info workflow.tracedir you'll get the same.

I think worflow.tracedir doens't exists.

[ewels]

Good find! 👍