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The input file extension matters

Open Midnighter opened this issue 2 years ago • 0 comments

Description of the bug

When providing a suitable input with a file extension of .tsv, the pipeline fails as shown below. However, when providing the same file with extension .txt the pipeline runs successfully. This was unexpected to me and the error message is not helpful.

Command used and terminal output

nextflow run \
    nf-core/fetchngs \
    -r '1.5' \
    --input 'test.tsv' \
    -profile docker \
    -resume

N E X T F L O W  ~  version 21.10.5
Launching `nf-core/fetchngs` [golden_avogadro] - revision: c318ae12fc [1.5]
                                               
ERROR: Validation of pipeline parameters failed!
                                                                                               
                                                                                               
Unknown method invocation `printExceptions` on NfcoreSchema type 
                                               
 -- Check script '/home/moritz/.nextflow/assets/nf-core/fetchngs/main.nf' at line: 20 or see '.nextflow.log' file for more details

Relevant files

test.tsv

SRR2231363
SRR2231379
SRR2195657

System information

  • Nextflow 21.10.5

Midnighter avatar Feb 10 '22 11:02 Midnighter