-profile test failing due to relative path in flowcell_input.csv

[jgbaum]

Description of the bug

As discussed in Slack, the test profile for this pipeline results in failure due to the relative path to the SampleSheet.csv in flowcell_input.csv. The pipeline seems to look for the SampleSheet.csv in a path relative to the current working directory.

Updating the path to the SampleSheet.csv to be absolute worked to resolve this issue, but there's probably a more generalizable solution. I'm new to nextflow / nf-core, so apologies if this should have been obvious.

Command used and terminal output

(nf-core-3.10.10) [jgbaum@node035 jgbaum]$ nextflow run nf-core/demultiplex -profile test,singularity --outdir test6
N E X T F L O W  ~  version 22.10.7
Launching `https://github.com/nf-core/demultiplex` [small_gates] DSL2 - revision: 8e42b6cb4e [master]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/demultiplex v1.1.0-g8e42b6c
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : small_gates
  containerEngine           : singularity
  launchDir                 : /mnt/hpcscratch/jgbaum
  workDir                   : /mnt/hpcscratch/jgbaum/work
  projectDir                : /home/jgbaum/.nextflow/assets/nf-core/demultiplex
  userName                  : jgbaum
  profile                   : test,singularity
  configFiles               : /home/jgbaum/.nextflow/assets/nf-core/demultiplex/nextflow.config

Workflow options
  skip_tools                : []

Input/output options
  input                     : /home/jgbaum/.nextflow/assets/nf-core/demultiplex/assets/inputs/flowcell_input.csv
  outdir                    : test6

Demultiplexing options
  demultiplexer             : bclconvert

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

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

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

* The pipeline
  https://doi.org/10.5281/zenodo.7153103

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

* Software dependencies
  https://github.com/nf-core/demultiplex/blob/master/CITATIONS.md
------------------------------------------------------
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:UNTAR                       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:UNTAR       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT  -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FASTP                       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FALCO                       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:MD5SUM                      -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:UNTAR                       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:UNTAR       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT  -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FASTP                       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FALCO                       -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:MD5SUM                      -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:MULTIQC                     -
No such file: /mnt/hpcscratch/jgbaum/assets/inputs/SampleSheet.csv

 -- Check script '/home/jgbaum/.nextflow/assets/nf-core/demultiplex/./workflows/demultiplex.nf' at line: 306 or see '.nextflow.log' file for more details

Relevant files

No response

System information

No response

[edmundmiller]

@drpatelh Can this be closed?

[grst]

Closing since no activity