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Add tableRemoveComments - #93

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LouisLeNezet merged 6 commits into
nf-core:mainfrom
LouisLeNezet:other_table_format
Sep 29, 2026
Merged

LouisLeNezet merged 6 commits into
nf-core:mainfrom
LouisLeNezet:other_table_format

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@LouisLeNezet

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I just encountered a table where data are stored in a .tbl.
I managed to make the content stable but the header comments differ.

So here is a small update to remove comments (opt-in option).

@LouisLeNezet LouisLeNezet self-assigned this Sep 28, 2026

@erikrikarddaniel erikrikarddaniel left a comment

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Reviewed with Claude Code.

A useful addition, and the test covers the new option on all four file types plus the new normalizeTable overloads.

Inline comments, none blocking:

  • The docs and CHANGELOG say all # lines are removed; the code removes only the comment lines at the top of the file.
  • Comments after the data are kept, e.g. the trailing block of HMMER --tblout.
  • Dropping the extension check in tableMD5 changes tableMD5Keys for everyone, not only users of the new option; worth a CHANGELOG line.

Comment thread CHANGELOG.md Outdated
Comment thread docs/usage.md Outdated
Comment thread src/main/java/nfcore/nftest/utils/TableUtils.java Outdated
Comment thread src/main/java/nfcore/nftest/utils/TableUtils.java
LouisLeNezet and others added 3 commits September 29, 2026 09:21
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
@LouisLeNezet
LouisLeNezet merged commit 87c3c49 into nf-core:main Sep 29, 2026
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3 participants