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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Circular generator crashes on bwa index when input fasta file does not end in .fasta #899

Closed scarlhoff closed 2 years ago

scarlhoff commented 2 years ago

Circular generator fails on bwa index when using hs37d5_MT_only.fa as reference input

Relevant lines of code: https://github.com/nf-core/eager/blob/43a239bd132b4a6ccf791d7052f537f3d22b700c/main.nf#L1349-L1361

nf-core/eager v.2.4.4 nextflow v.22.04.0.5697

command: nextflow run nf-core/eager -profile eva,archgen,MT_hs37 -c ~/eager2.config --input HPD_MT.tsv -r 2.4.4 -dsl1 -with-tower -name HPD_MT

error: Picked up _JAVA_OPTIONS: -XX:ParallelGCThreads=1 [bwa_idx_build] fail to open file 'hs37d5_MT_only_500.fasta' : No such file or directory

apeltzer commented 2 years ago

Yeah this would need a bugfix for DSL1. Other option is to wait for DSL2 version of EAGER or renaming your fasta to have .fasta extension for the time being.

jfy133 commented 2 years ago

@apeltzer can you review?

@scarlhoff could you test your original run but -r circularmapper-fix (make sure to use the original FASTA with the .fa extension)

scarlhoff commented 2 years ago

Circulargenerator and the whole run finished! 🥳