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I recently ran this workflow with a samplesheet that included the index column, but I had no index files, so I left this column blank. I did this because I interpreted that this would be required from the:
The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. If the index files are not available, the files will be automatically indexed during the pipeline run which can have an effect on the runtime.
When I tried to run the workflow with the first samplesheet, it seemed to stall right at the beginning, and none of the actual workflow processes started:
N E X T F L O W ~ version 23.04.2
Pulling nf-core/bamtofastq ...
downloaded from https://github.com/nf-core/bamtofastq.git
Launching `https://github.com/nf-core/bamtofastq` [elated_laplace] DSL2 - revision: c70f49b20c [2.1.0]
Downloading plugin [email protected]
WARN: The following invalid input values have been detected:
* --cpus: 4
* --single_cpu_mem: 6 GB
It's quite possible that this is an issue specific to our environment, and not reproducible when running locally - I'm not sure. However, I think if the docs were changed:
The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. If the index files are not available, the files will be automatically indexed during the pipeline run which can have an effect on the runtime.
to
The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 2 columns to match those defined in the table below. If the index files are not available, the files will be automatically indexed during the pipeline run which can have an effect on the runtime.
Then that might prevent this issue for others (at least, others at my organization 😄 ) in the future.
Description of the bug
I recently ran this workflow with a samplesheet that included the
index
column, but I had no index files, so I left this column blank. I did this because I interpreted that this would be required from the:Did not work: ega_samplesheet.csv
Did work: foo.csv
When I tried to run the workflow with the first samplesheet, it seemed to stall right at the beginning, and none of the actual workflow processes started:
It's quite possible that this is an issue specific to our environment, and not reproducible when running locally - I'm not sure. However, I think if the docs were changed:
Then that might prevent this issue for others (at least, others at my organization 😄 ) in the future.
Command used and terminal output
Relevant files
No response
System information
nextflow version: 23.04.2 build 5870
hardware: cloud (aws)
executor: awsbatch
container engine: docker (i think...)
bamtofastq version: 2.1.0
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