nextflow

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[Feature Request] Support for querying the SRA metadata using AWS Athena and Google BigQuery

14

## New feature The recent collaboration between `NCBI` and the cloud providers allows one to query the entire archive based on the metadata in AWS Athena. Here are some relevant...

abhi18av

`nextflow clean` throws `Unexpected error [EOFException]` when attempting to clean previous runs

2

## Bug report After a successful run of my pipeline, I am trying to clean the workspace from previous runs. I'm doing so using `nextflow clean -f -before nauseous_cajal`, which...

MatteoSchiavinato

Cache invalidated when $launchDir is used (no resume possible)

3

## Bug report I am not sure if this is a bug or feature, but it's definitely worth to mention, at least on https://www.nextflow.io/blog/2019/troubleshooting-nextflow-resume.html because I think that this behaviour...

tamasgal

## Bug report ### Expected behavior and actual behavior Versions containing dashes (`-`), such as `22.09.4-edge`, end up being reported without the dashes (`22.09.4-edge` becomes `22.09.4.edge`) ### Steps to reproduce...

tcrespog

Nextflow JAR download via wget fails with uninformative error message if certificates are missing

1

## Bug report ### Expected behavior and actual behavior On a system / in an environment where (by mistake) SSL / TLS certificates are not available, running the `nextflow` script...

simeoncarstens

Resolve relative paths against the work dir

6

Using nf-core pipelines as an example, by default we set `--outdir ./results` which is fine for shared file systems / HPC environments but with the growing adoption of Cloud this...

drpatelh

GLS support for mounting buckets with gcsfuse

1

## New feature Running gcsfuse in a docker container to mount a gs bucket requires the container either to be run with --privileged, or with --device=/dev/fuse --cap-add=SYS_ADMIN for it to...

sereeena

Channel might be mixed

1

## Bug report (input channel val field somehow is treated as path) ### Expected behavior and actual behavior (nextflow works with 50 sample, on the 51st sample, it trigger an...

kemin711

Dynamic directive : Label directive is not working

9

## Bug report Hello, From this script example: ``` vepVersionCh = Channel.from(1,2,3) process vep { label { "vep${version}" } input: val(version) from vepVersionCh """ echo ${version} """ } ``` Dynamic...

grafitos

Nextflow - SLURM job interface disconnect

16

## Bug report I am noticing a problem with the Nextflow-SLURM interface when processing large number of jobs. For example, I am running a workflow and have spawned ~10,000 tasks...

nickhsmith