Mapping with bowtie2 does not work

[teepean]

Hello!

I decided to test mapping with bowtie2 but ran into an error:

[-        ] process > makeFastaIndex -
[-        ] process > makeSeqDict    -
No such variable: bwa_index_bwamem

 -- Check script '.nextflow/assets/nf-core/eager/main.nf' at line: 1518 or see '.nextflow.log' file for more details

Running on Ubuntu 20.04 under WSL2. Both bwa aln and bwa mem work without issues.

Eager revision: f2a326d [dev]
Nextflow version 20.07.1 build 5412
Docker version 19.03.8, build afacb8b7f0

nextflow.log

[jfy133]

Thanks @teepean - I can replicate so will investigate!

[jfy133]

Note to self: this only occurs when the --bt2_index is supplied. Running bowtie2 without a pre-made index works without an issue.

[jfy133]

Issue is lines 834-891, where bwa_index_mem is only set to Channel.empty when BT2 indexing is requested.

[jfy133]

@teepean issue should be solved in an upcoming patch of 2.2! Will close this once that's out.

[teepean]

@teepean issue should be solved in an upcoming patch of 2.2! Will close this once that's out.

Thanks!

[jfy133]

@teepean should be in -r 2.2.1!

[teepean]

@teepean should be in -r 2.2.1!

It is working. Thank you!

[martinacaruso98]

jordwil/nextflow-bowtie2#1 (comment)

Is there anyone that can help?

[jfy133]

Hi @martinacaruso98 I'm sorry but you appear to be referring to another pipeline (based on the link you posted), we can't help with that.

[martinacaruso98]

Hi @martinacaruso98 I'm sorry but you appear to be referring to another pipeline (based on the link you posted), we can't help with that.

Oh, sorry! Thank you anyway!