Harshil Patel
Harshil Patel
### Description of the bug ``` The exit status of the task that caused the workflow execution to fail was: 1 Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)' Caused by: Process...
This pipeline won't work in offline situations because it needs to download metadata and fastq files from the web. We should probably add a check/warning/fail to make sure that there...
I cant seem to find `GraphMap2` on BioConda which also means the associated BioContainer wont exist. It would be nice to be able to use this in the pipeline because...
### Description of feature Context in [this Tweet](https://twitter.com/nilshomer/status/1498528699670433795?s=20&t=1uKZpUz-ZkBQKuCobNvyGQ). Used by @peterk87 @fmaguire in [this pre-print](https://www.biorxiv.org/content/10.1101/2022.02.22.481551v1). Be great if you can add a little description as to why hard-clipping was preferred...
### Description of feature Add tube map for both Illumina and ONT arms of pipeline.
For some reason the ref/alt bases initially displayed in the ASCIIGenome have disappeared in the [results](https://nf-co.re/viralrecon/2.1/output#asciigenome) from the [latest release](https://nf-core-awsmegatests.s3-eu-west-1.amazonaws.com/viralrecon/results-f0171324a60d1759ca7f5d02351372d97d22cc12/platform_illumina/variants/ivar/asciigenome/SAMPLE_10/SAMPLE_10.MN908947.3_6904_7004.pdf). Be good to figure out why and push a fix.
Custom configs are now hosted centrally at `nf-core/configs`. We need to think about where we host the documentation for running these config files. These are currently added on a per-pipeline...
I have now tested this with the rnaseq pipeline (v3.0) on my own fork. This means we can have remote genome configs for each Institution so all users can just...
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...
Similar to the existing 'nf-core modules info' command but for subworkflows.