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Bump cwltool from 3.1.202206231… (compare)
dependabot[bot] on pip
Bump cwltool from 3.1.202206231… (compare)
dependabot[bot] on pip
mr-c on master
Bump cwltool from 3.1.202206070… (compare)
mr-c on 4138
dependabot[bot] on pip
Bump cwltool from 3.1.202206070… (compare)
mr-c on master
cache results of cwltool versio… (compare)
hello! just curious about the code here : https://github.com/DataBiosphere/toil/blob/master/src/toil/cwl/cwltoil.py#L736
mutable is by default set to false, which means that there is no downloaded copy of the file (and a link to it is created instead). in the function call examples, there wasn't any explicit declaration of mutable to true, so do they exhibit "streamable" properties? what more changes should we make here?
streamable
is that you will get a pipe (a FIFO) presented to the tool instead of a normal file? I'm not really sure.
file_store.readGlobalFileStream
function, but that returns a Python file object, and doesn't currently produce a FIFO on disk. So I think getting CWL streamable support would involve handling streamable requests from CWL by using file_store.readGlobalFileStream
and producing a FIFO and a thread to fill it with data.
okay, i see! thank you 👍️ so we need to implement a FIFO process for
is that correct?
file_store.readGlobalFileStream
so any inputs regarding that would be much appreciated
Okay, thank you for the feedback!
I've made some changes - if it looks good, may I go ahead and submit the proposal?
FileNotFoundError: [Errno 2] No such file or directory: '_:file:///juno/work/access/testing/users/johnsoni/access_qc/work5/f26b1779cb2f5ea39419d80a2066faf9/e81b/360a/tmpb4cbwihh/out/simplex_bam_pool_a_dir'
toilfs:16305:0:files/for-job/kind-CWLJob/instance-7ousmklr/file-184521b84be2407b8ea6ef01398c6f81/histogram.pdf