-
### Description of feature
Hi, I couldn't run the pipeline on some smart-seq datasets which contains only single-end fastq files. I tried with two different samplesheets and get an error that fastq_2…
-
### Description of the bug
I ran "nextflow run nf-core/cutandrun -profile test,conda" command after installing conda and nextflow following the instruction and got the error message
### Command used…
-
### Description of the bug
Issue with latest Nextflow release.
This was a silent message before, it's now an error and fails the pipeline.
### Command used and terminal output
_No response_
### Re…
-
## Bug report
### Expected behavior and actual behavior
When running nextflow with `docker.sudo=true` and any env var in `envWhitelist` I expect the env vars to be available inside the process …
-
We need to modify the current release action so that upon release, the JSON file is used to eventually generate a PR for https://github.com/nextflow-io/plugins
-
### Description of the bug
What is "*assemblies_mqc.csv" and how can I create one? I have run my assembly on rnaspades (spades/3.15.5+dfsg-2) outside of the pipeline (with all samples together) and t…
-
Hi,
First thanks for developing this great tool!
I am trying to run the full SCENIC pipeline using Nextflow and docker on our AWS linux instance (m5.12xlarge) but the pipeline seems to get stuck…
-
Currently, we adhere to the [Nextflow core guidelines](https://nf-co.re/docs/contributing/guidelines#if-the-guidelines-dont-fit) in our Nextflow pipelines. However, since our pipelines are not part of…
-
Create a cookie cutter template based on nf-hello, with a command-line tool that allows the user to enter things like plugin name, target nextflow version, etc. Should make it easier to start a new pl…
-
### Description of feature
At least for v2.7.1, when running:
```bash
nextflow run main.nf \
--aligner cellrangermulti \
--skip_cellrangermulti_vdjref \
--skip_emptydrops \
--gex_frna_probe_…