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Fix conda #89

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d4straub wants to merge 51 commits into from
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Fix conda #89

d4straub wants to merge 51 commits into from

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@d4straub
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@d4straub d4straub commented Nov 12, 2025 •
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Attempting to fix conda environment of process KRAKEN2PREPARATION for #88
Intentionally against master branch for now to run relevant tests.

I fixed KRAKEN2PREPARATION but now RENAME_FASTQ_HEADERS_PRE fails. I am very much against downgrading this as well, because that might have performance impacts.
A change from minimum nextflow version 25.04.0 to 25.04.8 made KRAKEN2PREPARATION fail again...

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/detaxizer branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

d4straub and others added 30 commits August 7, 2025 11:45
@d4straub
bump version to 1.3.0dev
7557403
@d4straub
update nf-test snaps
c7aebf7
@nf-core-bot
[automated] Fix code linting
80a7e59
@d4straub
Merge pull request nf-core#79 from d4straub/bump-version-1.3.0dev
20e2569 
bump version to 1.3.0dev
@m3hdad
bbmap/filterbyname module added
0e1c541
@m3hdad
feat: add bbmap filter option
e6f74c2
@m3hdad
fix missing curly braces
6e36a00
@m3hdad
fix missing curly braces
ee2b83a
@m3hdad
fix single channel invocation for bbmap/filterbyname module
374ad20
@m3hdad
define filterbyname_remove ext.args in modules.conf
51e8907
@m3hdad
add rename&&remove to bbmap_filterbyname out names
111ee43
@m3hdad
modify changelog
1c33d30
@m3hdad
bbmap/filterbyname should drop reads it sees
93f5396
@m3hdad
filterbyname.sh removes isolated kraken2 IDs as substring of fastq he…
1fe5f61 
…ader
@m3hdad
update publish pattern to include single end reads.
b9eebd2
@m3hdad
map kraken2 seqids to fq headers by position
9bcea2d
@m3hdad
Align Kraken2 read IDs with FASTQ headers
0ca8e1a
@m3hdad
escape correctly
732bd35
@m3hdad
fix reviewer comments
f55f831
@d4straub
Merge pull request nf-core#80 from m3hdad/feature/new-filtering-tool
4d0d5de 
Feature/new filtering tool
@d4straub
update citations
aabdf32
@d4straub
update citations 2
d6b4f9f
@d4straub
fix rocrate_readme_sync
ca4bc8d
@d4straub
Merge pull request nf-core#81 from d4straub/update_publication
840df13 
update citations
@nf-core-bot
Template update for nf-core/tools version 3.4.1
6d091ee
@d4straub
merging template updates 3.4.1
7673b62
@d4straub
omit process count check
6f67ac8
@d4straub
fix release announcement
666d60e
@d4straub
fix rocrate_readme_sync
76d3cff
@d4straub
update multiqc file check
0a197f0
d4straub and others added 20 commits November 6, 2025 14:31
@d4straub @mashehu
Update nextflow.config
9e78dc2 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@d4straub
Merge pull request nf-core#84 from d4straub/merging-template-updates-…
658343a 
…3.4.1

Merging template updates 3.4.1
@d4straub
add codeowner file
d37a47d
@d4straub
Merge pull request nf-core#85 from d4straub/add-codeowners
34ddee2 
add codeowner file
@d4straub
nf-core modules update
cfe055a
@d4straub
fix bbduk diff, blast, snaps
6319715
@nf-core-bot
[automated] Fix code linting
3019b26
@d4straub
update multiqc files in snap's
82633dd
@d4straub
nf-core modules patch blast/blastn
6612abc
@d4straub
fix fastp input channel
2e57c8e
@d4straub
use fixed nf-core module blast/blastn
6921386
@d4straub
Merge pull request nf-core#86 from d4straub/modules-update
5282f9b 
nf-core modules update
@d4straub
bump version to 1.3.0
a7a0efe
@d4straub
fix typo in CHANGELOG
47ab3f6
@d4straub
update metro figure
eb477a8
@d4straub
Merge pull request nf-core#87 from d4straub/bump-version-1.3.0
783adc0 
bump version to 1.3.0
@d4straub
change conda packages
d27488b
@d4straub
downgrade ubuntu and tar
7c871f2
@d4straub
update tar version in snap
c0d4ad5
@d4straub
minimum nextflow version bump to 25.04.8
4e7ff30
@d4straub
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d4straub commented Nov 12, 2025

Ok, it might be the conda version. I misuse that PR here now for shameless testing and will later open a clean one.

@d4straub
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d4straub commented Nov 12, 2025

Closing due to too many useless commits. Its seems to be indeed the conda version.

@d4straub d4straub closed this Nov 12, 2025
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3 participants

@d4straub @nf-core-bot @m3hdad