A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

and I can approve on the nf-tests-plugins repo

```~/P/nft-utils version_bump_1.1.0 ❱ ./bump-version.sh 1.1.0                                                                                                  (base)
Bumping version to 1.1.0
sed: 1: "0,/&lt;version&gt;/{s/&lt;versio ...": bad flag in substitute command: '}'```
:sweat:

<https://github.com/nf-core/nft-utils/pull/82|github.com/nf-core/nft-utils/pull/82>

Do we want to attach a note about this in the release notes?
&gt; We will just need to announce that the sanitizeOutput fix will change the snapshot with unstableKeys usage on folder.

What should it say? I'm not clear on the exact change

• sanitizeOutput snapshot are to be updated due to fix on unstableKeys usage on folder

<https://github.com/nf-core/nft-utils/releases/tag/1.1.0|github.com/nf-core/nft-utils/…/1.1.0>

<https://github.com/askimed/nf-test-plugins/pull/37|github.com/askimed/nf-test-plugins/pull/37>

Am I gonna cause a big thing if I bump nft-utils in the modules repo?

Would love to use the new ignoreKeys option

<https://github.com/nf-core/modules/pull/12768|github.com/nf-core/modules/pull/12768>

I did it here

<@U039DEJ1RJS> have we created an issue in <#CE5LG7WMB> about the formatting?

I did not, I was waiting for Matthias’ response on my comment in the fgumi PR

He's on vacation, so let's create an issue so we don't forget about it

<https://github.com/nf-core/tools/issues/4452|github.com/nf-core/tools/issues/4452>

Just before anouncing the release and new features in shameless-promo, should we use  `unstablePattern*s*` or `unstablePattern` (with or without `s` ) ?

If it takes a list I would prefer with the s

Here is the fix and version bump
<https://github.com/nf-core/nft-utils/pull/83|github.com/nf-core/nft-utils/pull/83>
Would it be okay to do a small release ?
I wouldn't want the parameter to be used too much before changing it.

Do you want to make the release, or should I do it ?

Done on github
<https://github.com/nf-core/nft-utils/releases|github.com/nf-core/nft-utils/releases>

Is there something else to do ?

Need top update the nft plugins repo, e.g. :<https://github.com/askimed/nf-test-plugins/pull/37|github.com/askimed/nf-test-plugins/pull/37>

Done
<https://github.com/askimed/nf-test-plugins/pull/38|github.com/askimed/nf-test-plugins/pull/38>

OK, updated in my PR so we just get this version

Hi,
Here is a new PR to add some normalizing step for csv files:
<https://github.com/nf-core/nft-utils/pull/86|github.com/nf-core/nft-utils/pull/86>
This should allow to get md5sum even with some floating point differences.

Does this do tsv files too, but with the same `csvMD5Keys` name?

Good point, what would you suggest ?
`tableMD5Keys` ?

<@U016SFULDB8>: before making a release would tableMD5Keys be better ?

Here is the PR with the update to `tableMD5Keys`
<https://github.com/nf-core/nft-utils/pull/91|github.com/nf-core/nft-utils/pull/91>

Hi, I’m getting an error from `nft-utils` . Are there known incompatibilities?
```...

Load .nf-test/plugins/nft-utils/1.1.1/nft-utils-1.1.1.jar
Load .nf-test/plugins/nft-bam/0.7.0/nft-bam-0.7.0.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Warning: every snapshot that fails during this test run is re-recorded.
....
Could not find the nft-bam plugin.
WARNING: A compatible version of nft-bam is not available. Cannot calculate reads MD5 for BAM/SAM/CRAM files; output may be unstable.```

I'm sure I saw a note somewhere in the plugin docs to say that, but can't see it immediately

We have a release <https://github.com/nf-core/nft-utils/releases/tag/1.2.0>

I need aproval on <https://github.com/askimed/nf-test-plugins/pull/39>
so I can update the plugin on the modules repo

Hi,
Can I have a review with someone with write access on nft-utils ?
<https://github.com/nf-core/nft-utils/pull/93|github.com/nf-core/nft-utils/pull/93>
I would also like to make a release so that I could fix the test in <https://github.com/nf-core/modules/pull/13045|github.com/nf-core/modules/pull/13045>

Thanks !
I forgot to bump the version
<https://github.com/nf-core/nft-utils/pull/94|github.com/nf-core/nft-utils/pull/94>

Do you need help into doing the PR to <https://github.com/askimed/nf-test-plugins>?

Should be ready
<https://github.com/askimed/nf-test-plugins/pull/40|github.com/askimed/nf-test-plugins/pull/40>

Hey, could I get a review here? <https://github.com/askimed/nf-test-plugins/pull/41|github.com/askimed/nf-test-plugins/pull/41>

<@UQZG2UCF3> could you also hit the merge button? apparently write access is needed

What was the reasoning behind making `getAllFilesFromPath` output only relative paths?

for me the reasoning was we need relative path, because we ran locally and CI, and I don't want failure.
we could add this as an option indeed

Yes but this no longer creates valid md5sums, right? Or am I using the wrong function for that?

this is what we have in sarek:
```        // stable_name: All files + folders in ${outdir}/ with a stable name
        def stable_name = getAllFilesFromPath(outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
        // stable_content: All files in ${outdir}/ with stable content
        def stable_content = getAllFilesFromPath(outdir, ignoreFile: 'tests/.nftignore', ignore: [scenario.ignoreFiles])```

so with relative: true, and includeDir you get just filenames with relative paths

have a look at what we all managed here: <https://github.com/nf-core/sarek/blob/dev/tests/lib/UTILS.groovy>

oh! I must have made a mistake then. I'll see if I can get it working

<@U03UCQH8FN2> any reason about the nextflow pin in the conda environment.yml?
cf <https://github.com/nf-core/nft-utils/pull/96/changes>