Hello, I am having some trouble running the rnasplice test profile. I am receiving the following error:

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --fasta: the file or directory '<https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/X.fa.gz>' does not exist.
* --input: the file or directory '<https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv>' does not exist.

I am using this command to initiate the test:

nextflow run nf-core/rnasplice -r 1.0.4 -profile test,docker --outdir out/

. Other nf-core pipelines are running fine (e.g., nf-core/rnaseq). In my .nextflow.log file I noticed the following:

Sep-09 14:57:00.653 [main] DEBUG n.file.http.XFileSystemProvider - Got HTTP error=404 waiting for 250ms (attempt=1)
Sep-09 14:57:00.935 [main] DEBUG n.file.http.XFileSystemProvider - Got HTTP error=404 waiting for 750ms (attempt=2)
Sep-09 14:57:01.719 [main] DEBUG n.file.http.XFileSystemProvider - Got HTTP error=404 waiting for 2250ms (attempt=3)
Sep-09 14:57:17.685 [main] ERROR nextflow.validation.SchemaValidator - ERROR: Validation of pipeline parameters failed!

I also went to https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv on my browser and I am getting a 404 message there as well, so I'm thinking this error is not caused by an issue with my Nextflow setup. Any advice/assistance would be much appreciated. Thanks!

I also get a 404 with that link to the CSV file for rnasplice, but it works fine with

.../rnaseq/...

, so something seems wrong with the test data. The test data is only needed for a quick test. If you have your own data, I would test with that. If you want a quick test, you can just pick a treatment and a control sample and maybe downsample the FASTQ to 100k-1M reads. You won't get any significant results, but you'll see if you run into errors or not.

Thank you, I'll try running rnasplice on a small test dataset of my own. Also looping in @Jared Khan here who was experiencing the same issue. Thanks again Thomas!

+1 I am also running into the same issue. Running on my own data as well so fingers crossed. I usually rely on the test profile to ensure the at the a minimum the pipeline runs as intended (technical control) before breaking it with my settings 🙂

Don't recall coming across that one; make sure you use absolute paths. If you can't figure it out, maybe let us know more details (command, configuration, failing process, detailed messagesm aybe even the

.nextflow.log

). 🤞

Yeah, it's a weird one. You might be on to something with the paths - I fixed it by changing / removing some - but those were all direct <s//3|s3&gt;// paths, so no idea what's up. Maybe trailling "/" are an issue, but who knows.