Closed emsisson closed 8 months ago
Pasting URL https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/main.nf into web browser on desktop computer fails, also.
This likely results from GitHub API rate limits. Are you in a network environment where there might be many people simultaneously trying to access resources through the GitHub API?
I do work for a large academic medical center (roughly 24,000 FTEs), and I certainly do not know everything that everybody else is doing, so it is possible. Do you recommend that I try again outside normal working hours?
I tried again this morning about 7:20 AM local time, and I saw the same result.
Then I entered URL https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/main.nf into the web browser on my iPad. While my computer connects via VPN to my employer's network, the iPad connects to the Internet through my residential ISP and not through the VPN. That failed, also; see attached screenshot.
Are you certain that the file is present and that some redirect mechanism is not intercepting requests for it?
Having the same issue
Edit: There's a typo in the example, missing a s at the end of 'transcriptome'
nextflow run epi2me-labs/wf-transcriptome
Edit: There's a typo in the example, missing a s at the end of 'transcriptome'
nextflow run epi2me-labs/wf-transcriptome
Oh, well spotted. Thanks
The demo command has been updated and is now visible on the prerelease
branch. Closing ticket.
The fix works for me, also. Thank you.
Operating System
Other Linux (please specify below)
Other Linux
RHEL 8.7
Workflow Version
wf-transcriptomes/1.0.0 nextflow/23.04.3
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-transcriptome \ --fastq differential_expression/differential_expression_fastq \ --de_analysis \ --ref_genome differential_expression/hg38_chr20.fa \ --transcriptome-source reference-guided \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --direct_rna \ --minimap2_index_opts '-k 15' \ --sample_sheet differential_expression/sample_sheet.csv \ --jaffal_refBase differential_expression/chr20/ \ --jaffal_genome hg38_chr20 \ --jaffal_annotation genCode22 \ -profile singularity \ -without-docker \ -with-singularity wf-transcriptomes.sif
Workflow Execution - CLI Execution Profile
singularity
What happened?
Received series of messages CAPSULE: Downloading dependency ... ending with
N E X T F L O W ~ version 23.04.3
Pulling epi2me-labs/wf-transcriptome ... WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/nextflow.config Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/main.nf
Relevant log output
Application activity log entry
No response