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ncbi / sra-human-scrubber

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
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Docker image is missing ps #31

Open maxlcummins opened 1 month ago

maxlcummins commented 1 month ago

Hi!

The docker image does not contain ps which makes it incompatible with nextflow runs which capture performance metrics for processes.

Command 'ps' required by nextflow to collect task metrics cannot be found.

Similar to this issue: https://forum.qiime2.org/t/docker-container-not-fully-compatible-with-nextflow/18699,

maxlcummins commented 1 month ago

For others who may struggle with this issue try this or a similar image via biocontainers:

'quay.io/biocontainers/sra-human-scrubber:2.2.1--hdfd78af_0'

https://biocontainers.pro/tools/sra-human-scrubber

durbrow commented 1 month ago

That looks like nextflow's problem.

Generally, a docker image provides the minimum necessary, they try to be small. It is standard to derive your own image from an existing one and add to it.

maxlcummins commented 1 month ago

Hi @durbrow - a fair point, thanks for your response. Thought it was worth a note given compatibility with nextflow is desirable for many.

Feel free to close the issue