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Eco-Flow / excon

A pipeline to measure gene family expansion and contraction
MIT License
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Singe NCBI download addition orthofinder does not work #45

Closed chriswyatt1 closed 2 months ago

chriswyatt1 commented 2 months ago

Command:

nextflow run main.nf -resume -profile docker,test_bacteria
WARN: Input tuple does not match tuple declaration in process `ORTHOFINDER_GO` -- offending value: [/excon/data/bacteria_data/Pseudomonas_aeruginosa.fasta, /workspace/excon/work/cd/2b316b6fd90c364f56834f483c60b8/Mycoplasmoides_pneumoniae.prot.fa.largestIsoform.fa, /workspace/excon/work/05/16491a5e60a651c8f86a9ceae90986/Mycoplasmoides_gallisepticum.prot.fa.largestIsoform.fa, /workspace/excon/work/2d/37851de48023aa770fa158a35eaa36/Mycoplasmoides_fastidiosum.prot.fa.largestIsoform.fa, /workspace/excon/work/d4/4fcde5a3efb961e06681261f1aa851/Mycoplasmoides_genitalium.prot.fa.largestIsoform.fa]
ERROR ~ Error executing process > 'ORTHOFINDER_GO'

Caused by:
  File `/excon/data/bacteria_data/Pseudomonas_aeruginosa.fasta` is outside the scope of the process work directory: /workspace/excon/work/a0/b5a2b3bcba6f01191ebe3a6f5d0741
chriswyatt1 commented 2 months ago

Sorted in 298f8e0