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Nextflow doesn't match the container from the withName section at the nextflow.config file (NFX_VERSION >= 22.03.0-edge).

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## Bug report When using containers specified in the `nextflow.config` file (`withName` section), Nextflow doesn't match them properly in versions `>= 22.03.0-edge`. ### Expected behavior and actual behavior - **EXPECTED**:...

CarlosLopezElorduy

pbspro: ignore resource directives if -l option is specified

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Closes #2264 Alternative solution to #2971 This PR changes the pbspro executor to ignore `cpus` and `memory` directives if `clusterOptions` contains `-l`. That way, you can do something like: ```...

bentsherman

Closes #2981 I basically just updated the `set` operator to return the input channel directly, for each channel type it supports. I'm not sure if that's the correct way to...

bentsherman

Add `k8s.cpuLimits` config option

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Closes #773 and #785 This PR adds the ability to specify request/limit values for resource directives (cpus, memory, time, accelerator). In Kubernetes, request/limit values correspond to request and limit in...

bentsherman

Add MaxErrorRetry to k8s-config (replace hardcoded 5 maxRetry)

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naineshmp

Support for EC-encrypted client keys (k8s)

3

Dear Nextflow maintainers, at MNM Diagnostics, your tool is widely used for genomic analyses. Quite recently, we found out that our Rancher configuration is incompatible with Nextflow; namely, the default...

pawelpiatkowski1125

Exit error message not printed to screen when used between process input brackets.

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## Bug report When using `exit , `, the message is not printed to the screen when it is between process input brackets. ### Expected behavior and actual behavior The...

mahesh-panchal

better error messages

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Nextflow is great!, But, it is sometimes quite difficult to debug nextflow errors due to uninformative error messages. Here is one example: ``` nextflow.enable.dsl=2 process wtf { input: val(a) val(b)...

brentp

Unexpected warning message

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After upgrading to JGit 6.1, the following warn message is reported in the log file. ``` Jun-08 19:01:52.220 [main] WARN org.eclipse.jgit.util.FS - Cannot run program "[?7h/usr/bin/git" (in directory "[?7h/usr/bin"): error=2,...

pditommaso

No such file in stdout instead of stderr

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## Bug report ### Expected behavior and actual behavior Some messages in terminal are printed in stdout instead of stderr. For example, when there is a missing file, the error...

Qwarctick