Remove trailing slash from params.igenomes_base

[pansapiens]

Check Documentation

I have checked the following places for your error:

• [*] nf-core website: troubleshooting
• [*] nf-core/rnaseq pipeline documentation

Description of the bug

S3 URL to iGenomes reference and annotations listed in pipeline_info/pipeline_report.html and pipeline_info/pipeline_report.txt are invalid. They contain an additional slash which makes them incompatible with some tools used to download files from S3.

Steps to reproduce

Run the pipeline with a flag like: --genome GRCm38.
Observe the output in pipeline_info/pipeline_report.html.

Expected behaviour

URLs in pipeline_info/pipeline_report.html and pipeline_info/pipeline_report.txt should be like:

s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa

but instead contain an additional slash:

s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa (note the extra slash between igenomes//Mus_musculus).

These URLs fail when used directly with the aws s3 commandline tool (v1.18.121) unless the additional slash is removed.

Nextflow Installation

Nextflow version: 21.04.0
Nextflow build: 5552
Pipeline version (commit on master): 0fcbb0a

Additional context

This is likely a result of the default value of igenomes_base here having a trailing slash, so that when it is used here a double slash is introduced. I've not yet tested if removing the trailing slash from igenomes_base fixes the issue without breaking other parts of the pipeline.

[drpatelh]

Thanks @pansapiens ! Yes, was fixed here in the pipeline template and needs to be fixed in this pipeline too. It should have come through via the automated sync mechanism we have but probably something I missed.

[drpatelh]

Fixed in #647