File not found error when using downloaded kraken2_db

[artefaritaKuniklo]

Describe the bug

when I use downloaded kraken2 database and put the archive in some place and run the pipeline with --kraken2_db parameter,
the process kraken2_db_preparation reported a bug which is caused by file not found

Steps to reproduce

$ nextflow run nf-core/mag --reads '../data/*_{1,2}.fastq' --busco_reference bacteria_odb9.tar.gz --task.memory 120 --task.cpus 32 -profile docker --kraken2_db minikraken2_v2_8GB_201904.tgz
....
Error executing process > 'kraken2_db_preparation (1)'                                        `bash .command.run`

Caused by:
  Missing output file(s) `minikraken2_v2_8GB_201904/*.k2d` expected by process `kraken2_db_preparation (1)`

Command executed:

  tar -xf "minikraken2_v2_8GB_201904.tgz"

Command exit status:
  0

Command output:
  (empty)

Work dir:
  /home/stella/Proj/20200908_NF/run/work/2a/aa7e195cef0882b13f789c378442af

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

and I am sure that this bug is caused by the different folder name in the archive and the base name of the archive

➜   tree ./minikraken2_v2_8GB_201904_UPDATE 
./minikraken2_v2_8GB_201904_UPDATE
├── database100mers.kmer_distrib
├── database150mers.kmer_distrib
├── database200mers.kmer_distrib
├── hash.k2d
├── opts.k2d
└── taxo.k2d

when the pipeline tried to find minikraken2_v2_8GB_201904/*.k2d, there is only minikraken2_v2_8GB_201904_UPDATE

System:

• Hardware: Dell Server R720
• OS:

➜  uname -a
Linux hal9003 5.4.0-47-generic #51-Ubuntu SMP Fri Sep 4 19:50:52 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

• Executor: local execute within tmux

Nextflow Installation:

• Version: N E X T F L O W ~ version 20.07.1+nf-core/mag version 1.0.0

[d4straub]

Hi there, thanks for reporting this.

The pipeline expects that extraction of minikraken2_v2_8GB_201904.tgz yields a folder minikraken2_v2_8GB_201904 with the respective database files. The tgz archive you are using however contains a folder with a different name. To fix this, you could just rename the tgz file to match the folder name, i.e. minikraken2_v2_8GB_201904.tgz -> minikraken2_v2_8GB_201904_UPDATE.tgz. I haven't tested that, but I think that should work.

This should be actually fixed in the dev branch, see #54.

[artefaritaKuniklo]

okay， I have already fixed it and I will submit a pull soon

[d4straub]

I appreciate your effort, but as I said, it is fixed already.

[artefaritaKuniklo]

oh sorry, I just forgot that