nextflow

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A top-level `bin` folder with hidden files (e.g. `.gitkeep`) results in failure on cloud based runs

3

### Steps to reproduce: 1. Create a `bin` directory and add a `.gitkeep` file to instruct git to track it (example here https://github.com/abhi18av/hello/tree/empty-bin) 2. Run the pipeline on S3 backed...

abhi18av

Change k8s client to use namespace and service account from nextflow config

8

Closes #2266

bentsherman

Tested in local and all seems to work closes #2492 Signed-off-by: Jorge Aguilera

jorgeaguileraseqera

Hi!, I'm having issues figuring out a bug within my code. While I produce a file_pair channel using the Channel.fromFilePairs al follow: "ch_fastq_file_path = Channel.fromFilePairs( params.fastq_file_path + '/*.R{1,2}.fastq.gz',checkIfExists:true) " When...

fgualdr

Closes #3184

kanor1306

improve docs

2

- Add -f, -fields to log CLI help - Remove whitespace - Fix typo in aws.rst

mribeirodantas

Fusion support for the azure batch task handler is trickier because much of the task logic (container options, environment vars, submit command) are handled in a separate class `AzBatchService`. So...

bentsherman

Add fusion support to grid executors

6

The strategy here is to create a secondary wrapper script that generates the container launch command, and pipes this script into the executor submit command. Just need to confirm that...

bentsherman

Signed-off-by: Lehmann-Fabian

Lehmann-Fabian

Currently, Nextflow is not compiling scripts with debug information and parsing all scripts as text so the GroovyCompiler is not able to include variable names in the generated binary This...

jorgeaguileraseqera