Pipeline test is failing

[davidecarlson]

Description of the bug

The test profile for the pipeline is failing to run on my HPC cluster. This does not happen with other nf-core pipelines (e.g., rnaseq). The log file (attached) is showing HTTP errors.

Command used and terminal output

nextflow run nf-core/rnavar -profile test,seawulf --outdir /gpfs/scratch/decarlson/rnavar_test

N E X T F L O W  ~  version 23.04.0
Launching `https://github.com/nf-core/rnavar` [festering_banach] DSL2 - revision: 222d7a15f7 [master]


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnavar v1.0.0
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Core Nextflow options
  revision                  : master
  runName                   : festering_banach
  containerEngine           : singularity
  launchDir                 : /gpfs/home/decarlson
  workDir                   : /gpfs/home/decarlson/work
  projectDir                : /gpfs/home/decarlson/.nextflow/assets/nf-core/rnavar
  userName                  : decarlson
  profile                   : test,seawulf
  configFiles               : /gpfs/home/decarlson/.nextflow/assets/nf-core/rnavar/nextflow.config

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet.csv
  outdir                    : /gpfs/scratch/decarlson/rnavar_test

Reference genome options
  genome                    : WBcel235
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict
  gtf                       : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf
  read_length               : 150
  known_indels              : https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  dbsnp                     : https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  snpeff_db                 : WBcel235.99
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans
  vep_cache_version         : 104

Alignment options
  star_index                : https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/index/star/star.tar.gz
  star_twopass              : true

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  config_profile_contact    : David Carlson (@davidecarlson)
  config_profile_url        : https://it.stonybrook.edu/services/high-performance-computing

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/rnavar for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/rnavar/blob/master/CITATIONS.md
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ERROR ~ Unable to read script: '/gpfs/home/decarlson/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf' -- cause: https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet.csv

 -- Check script '.nextflow/assets/nf-core/rnavar/main.nf' at line: 49 or see '.nextflow.log' file for more details

Relevant files

nextflow.log

System information

nextflow version 23.04.0.585
Hardware: HPC
Executor: Slurm
Container: Singularity
OS: Rocky Linux
version of nf-core/rnavar: v1.0.0

[spencermcminn]

I am getting this same error running on HPC using singularity:

Unable to read script: '/home/mcminns/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf' -- cause: https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet.csv

I am also getting this csv reading error when I use the same csv file that works for RNAseq.

[SpikyClip]

I'm getting the same issue. Essentially the expected branch for the test-data repo is not there. This should be a quick fix?

[nvnieuwk]

The rnavar test data branch has been restored, sorry about the issues this caused