23.10.0 comparison (testing) #23
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Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Rob Syme <rob.syme@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
…4056) Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Justin Herr <justinherr.cs@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
…extflow-io#4046) Signed-off-by: Florian De Temmerman <florian.detemmerman@lizard.bio>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Duncan Parkes <duncan.parkes@gmail.com>
…ow-io#4067) Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
This commit add the `cpu_model` in the Nextflow trace record. Note: the field is not included in the default trace file, but it can be added by adding in the nextflow config the setting ``` trace.fields = '..,cpu_model' ``` Signed-off-by: Sabrina Krakau <sabrinakrakau@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Fritjof Lammers <25619971+mobilegenome@users.noreply.github.com> Signed-off-by: Fritjof Lammers <fritjof.lammers@vogelwarte.ch> Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Ben Sherman <bentshermann@gmail.com>
nxf_parallel runs a number of processes in parallel, distributing them across a limited number of workers. Prior to PR nextflow-io#1884, errors were not being checked. PR#1884 was intended to remedy this but effectively only checked the _last_ command to exit (which was, unfortunately the case that was tested for). Processes that exit while there is still work going on were not being "waited" on, so their exit status was not being checked, and failures were escaping unnoticed. This commit: - updates the loop that's tracking the work so that it waits on processes that have exited; and - updates the test cases so that the failing command is _not_ the last in the list and ensures that the templated text is as expected. Signed-off-by: George Hartzell <hartzell@alerce.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
This commit adds the -cloudcache run command line option that allows storing Nextflow cache metadata into a cloud object storage bucket instead of storing them in the local .nextflow directory. The target cloud cache path is specified as command line argument, e.g. -cloudcache s3://bucket-name/path. Moreover, this commit allows controlling the cloudcache via the nextflow.config file as shown below: ``` cloudcache.enabled = true|false cloudcache.path = '<some object storage path>' ``` Supported object storage are AWS S3, Azure Blob storage and Google Storage. Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
This commit allows disabling the privileged container execution when using the fusion file system. This can be controlled by using the following configuration setting: ``` fusion.privileged = true|false // default true ``` The effective use of this setting depends on the target execution. Currently, it's only supported by the Kubernetes executor which requires the use the k8s-fuse-plugin to be installed in the target cluster More details here https://github.com/nextflow-io/k8s-fuse-plugin Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Phil Ewels <phil.ewels@seqera.io> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
…o#4400) [ci fast] Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Co-authored-by: Rory Nolan <rory@mirvie.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Phil Ewels <phil@seqera.io> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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