fermikit: avoid writing to inputdir

[pavanvidem]

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[bernt-matthias]

Please bump the tool version.

According to #3991 there are two fermi related tools writng to the input dir

• fermi2 .dat.fai
• fermikit_variants .dat.fai

[pavanvidem]

fermi2 does not take any FASTA input to generate an index file. I tested it on my local Galaxy instance there was no .fai generated. Can you please check again if it is true?

[bernt-matthias]

This is the files dir after the planemo test ran (not on your branch .. but the current master):

tree /tmp/tmp95f1wuat/files/
/tmp/tmp95f1wuat/files/
├── 3
│   └── 1
│       └── a
│           └── dataset_31af8b95-c287-4943-904f-21255c8da5b3.dat
├── 4
│   └── 3
│       └── d
│           └── dataset_43dc1578-7d1d-4d6f-8069-48b76cf964ca.dat
├── 8
│   └── a
│       └── f
│           └── dataset_8af2c39a-323c-4f0c-b6ac-e26c2da79a00.dat
├── 9
│   ├── c
│   │   └── d
│   │       └── dataset_9cd20b5f-73cd-46c9-b396-6ecaf5cb9497.dat
│   └── d
│       └── 5
│           ├── dataset_9d5b6381-6a77-4006-b8db-0a3158bcf3d5.dat
│           └── dataset_9d5b6381-6a77-4006-b8db-0a3158bcf3d5.dat.fai
├── d
│   └── 7
│       └── d
│           └── dataset_d7df0b0c-9363-4630-847d-42d34196b14d.dat
└── _metadata_files
    └── 3
        └── d
            └── d
                └── metadata_3dd1b444-14dd-4528-908d-f02f1b80f68f.dat

I guess its coming from this call
htsbox abreak -bcuf '/tmp/tmp95f1wuat/files/9/d/5/dataset_9d5b6381-6a77-4006-b8db-0a3158bcf3d5.dat'

[pavanvidem]

htsbox abreak -bcuf $ref call exits only in fermikit_variants tool, not in fermi2. In that case, it should be fixed in this PR.

We had a small discussion on silent update here: #3951 (comment)

[bernt-matthias]

Is the tool also wring to the locations specified in the data table?

[bernt-matthias]

When checking the diff it seems that this PR has been implemented meanwhile. Closing this.