bwa index not working

[ShixiangWang]

Description of the bug

The bwa index option pattern is not matching. https://nf-co.re/circdna/1.0.1/parameters#bwa_index It seems .alt file is not bwa index output.

-rwxrwxrwx  1 GuoHuangChun GuoHuangChun 2.9G Aug 13  2022 genome.fa
-rw-rw-r--  1 wsx          wsx           17K Feb 15 17:39 genome.fa.amb
-rw-rw-r--  1 wsx          wsx           954 Feb 15 17:39 genome.fa.ann
-rw-rw-r--  1 wsx          wsx          2.9G Feb 15 17:38 genome.fa.bwt
-rwxrwxrwx  1 zhaoqi       zhaoqi       1.1K Feb 15 16:57 genome.fa.fai
-rw-rw-r--  1 wsx          wsx          737M Feb 15 17:39 genome.fa.pac
-rw-rw-r--  1 wsx          wsx          1.5G Feb 15 17:55 genome.fa.sa

Command used and terminal output

Launching `https://github.com/nf-core/circdna` [mighty_saha] DSL2 - revision: 4f03e2641b [dev]

ERROR: Validation of pipeline parameters failed!

* --bwa_index: string [/data1/database/human/hg38/genome.fa.alt] does not match pattern ^\S+\.\{alt,amb,ann,bwt,pac,sa\}$ (/data1/database/human/hg38/genome.fa.alt)

### Relevant files

_No response_

### System information

_No response_

[DSchreyer]

I believe this should be sorted now when the new version is out (v.1.0.2). Thanks for bringing this to my attention.

[ShixiangWang]

@DSchreyer Tried the update version

ERROR: Validation of pipeline parameters failed!

* --bwa_index: string [/data3/wsx/aa_data_repo/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.amb] does not match pattern ^\S+\.\{amb,ann,bwt,pac,sa\}$ (/data3/wsx/aa_data_repo/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.amb)

[Yippee3]

The same error is reported in version 1.0.4 ERROR ~ * --bwa_index: string [/home/genome/index/bwa/GRCm39] does not match pattern ^\S+\.\{amb,ann,bwt,pac,sa\}$ (/home/genome/index/bwa/GRCm39)