A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hello! I've been having trouble getting fetchngs to complete today. When using the `apptainer` profile the full error message reads:
```ERROR ~ Error executing process &gt; 'NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (1)'

Caused by:
  Cannot invoke "nextflow.util.Duration.toMillis()" because "this.pullTimeout" is null```
The pipeline doesn't appear to get far enough to generate any files in a work directory but I found the following line in the `.nextflow.log` file:
```Caused by: java.lang.NullPointerException: Cannot invoke "nextflow.util.Duration.toMillis()" because "this.pullTimeout" is null ```
I'm not sure if this issue is related to apptainer or fetchngs, but any guidance would be appreciated!

I've tried to run using the `singularity` profile instead, but it fails at `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP` with the error:
```Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  WARNING: Skipping mount /var/lib/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container                                                                                 wget: unable to resolve host address '<http://ftp.sra.ebi.ac.uk|ftp.sra.ebi.ac.uk>' ```