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Release 2.4.0 #181

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merged 92 commits into from
Nov 18, 2024
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cfe8253
Replaced local unicycler module with nf-core module.
FloWuenne Jun 26, 2024
24f0cbc
Removed deprecated unicycler parameters from test_dfast.
FloWuenne Jun 27, 2024
2baeb3b
Updated CHANGELOG.
FloWuenne Jun 27, 2024
e922812
Removed no longer needed unicycler local files.
FloWuenne Jun 27, 2024
03f0dc8
Merge pull request #150 from FloWuenne/unicycler_nfcore
FloWuenne Jun 28, 2024
a49930e
fix missing dev tag in bumped version
Daniel-VM Jul 10, 2024
24ec64c
Merge pull request #152 from Daniel-VM/dev
Daniel-VM Jul 10, 2024
04091a3
remove files_unchanged items form linting
Daniel-VM Jul 10, 2024
1bb3278
fix files_unchanged to make a proper linting check
Daniel-VM Jul 10, 2024
b73c536
added changelog #153
Daniel-VM Jul 10, 2024
cc1882b
Merge pull request #153 from Daniel-VM/dev
Daniel-VM Jul 10, 2024
e8442e2
fix kmerfinder script to download reference
Daniel-VM Jul 10, 2024
3bfab15
add more resources to kmerfinder module to avoid memory related issues
Daniel-VM Jul 10, 2024
3e9cf3f
added changelog #154
Daniel-VM Jul 10, 2024
20830af
Merge pull request #154 from Daniel-VM/fix_kmerfinder_scripts
Daniel-VM Aug 28, 2024
084fec4
fixed current zenodo url to kmerfinderdb
Daniel-VM Aug 29, 2024
82adb62
update changelog in #157
Daniel-VM Aug 29, 2024
5f64486
Merge pull request #157 from Daniel-VM/fix_kmerfinderdb
Daniel-VM Aug 30, 2024
04def18
enhance KmerFinder support parsing multiple file format versions
Daniel-VM Aug 29, 2024
9280f89
update kmerfinderdb description
Daniel-VM Aug 29, 2024
b5b0407
update kmerfinder module
Daniel-VM Aug 30, 2024
fd7dd01
update kmerfinder module dir structure
Daniel-VM Aug 30, 2024
c2a94d7
update module paths and handle memory-errors in kmerfinder
Daniel-VM Aug 30, 2024
9e85db0
Merge pull request #159 from Daniel-VM/update_kmerfinder
Daniel-VM Sep 2, 2024
6250ad3
fix memory issues due to config in kmerfinder
Daniel-VM Sep 3, 2024
09a1eb6
Handle KmerFinder results when no species hit is detected
Daniel-VM Sep 3, 2024
ae525c0
handle prokka/bakkta channel when fasta file is empty
Daniel-VM Sep 3, 2024
fcf0ab9
update changelog in #160
Daniel-VM Sep 3, 2024
c66630f
Merge pull request #160 from Daniel-VM/dev
Daniel-VM Sep 3, 2024
41fd8c9
fix saving merged fastq files in fastp module
Daniel-VM Sep 5, 2024
7f438ec
#163
Daniel-VM Sep 5, 2024
f1f915c
extend description on save_merged param
Daniel-VM Sep 6, 2024
6e0d781
Fix CHANGELOG.md #163
Daniel-VM Sep 6, 2024
feaf603
Merge pull request #163 from Daniel-VM/dev
Daniel-VM Sep 6, 2024
488b5ab
append fastqc trim section to multiqc report
Daniel-VM Sep 13, 2024
b308a95
update multiqc config files to arrange preprocessing sections
Daniel-VM Sep 13, 2024
235bf18
update changelog #166
Daniel-VM Sep 13, 2024
7842632
fix prettier #166
Daniel-VM Sep 13, 2024
ed12940
Merge pull request #166 from Daniel-VM/multiqc_after_filtering_qc
Daniel-VM Sep 17, 2024
3045163
remove prams.save_merged from this pipeline
Daniel-VM Sep 10, 2024
8adff80
update CHANGELOG in #167
Daniel-VM Sep 17, 2024
05e784a
Merge pull request #167 from Daniel-VM/dev
Daniel-VM Sep 17, 2024
37488ee
fix wrong metadata in canu input channel
Daniel-VM Sep 17, 2024
a65648e
updated changelog in #168
Daniel-VM Sep 17, 2024
1cb4574
Merge pull request #168 from Daniel-VM/fix_canu_assembler
Daniel-VM Sep 18, 2024
8bf71a8
fixed input channel to minimap2_align
Daniel-VM Sep 17, 2024
663a770
refactor longread polishing and update medaka
Daniel-VM Sep 18, 2024
92bcfde
add condition to run miniasm on long/hybrid mode only
Daniel-VM Sep 18, 2024
fc6c0b9
Refined polishing step by 1-removing short reads; 2- selecting the po…
Daniel-VM Sep 20, 2024
c5c32d5
restricted the polishing step to long reads mode
Daniel-VM Sep 20, 2024
0917bda
update changelog in #169
Daniel-VM Sep 23, 2024
3f6a42d
Merge pull request #169 from Daniel-VM/fix_nanopolish_ont
Daniel-VM Sep 28, 2024
db3eb59
Template update for nf-core/tools version 3.0.0
nf-core-bot Oct 8, 2024
75ef2ec
Template update for nf-core/tools version 3.0.1
nf-core-bot Oct 9, 2024
4a10f2a
Template update for nf-core/tools version 3.0.2
nf-core-bot Oct 11, 2024
6b526ea
Merge branch 'dev' into nf-core-template-merge-3.0.1
Daniel-VM Oct 11, 2024
1cf3bd7
Merge branch 'dev+nf-core-template-merge-3.0.1' into nf-core-template…
Daniel-VM Oct 11, 2024
efbade0
mv fastp to older version due to inconsistency with fastq_trim_fastp_…
Daniel-VM Oct 11, 2024
b86a1a8
update CHANGELOG in #176
Daniel-VM Oct 11, 2024
2083999
Apply suggestions from code review
Daniel-VM Oct 15, 2024
8a8182a
[automated] Fix code linting
nf-core-bot Oct 15, 2024
5fbe68d
Merge pull request #176 from Daniel-VM/nf-core-template-merge-3.0.2
Daniel-VM Oct 15, 2024
cc0ae3a
added module cat_fastq
Daniel-VM Aug 29, 2024
b2ab59c
fix wrong variable naming
Daniel-VM Aug 29, 2024
1f2b944
update changelog #158
Daniel-VM Aug 29, 2024
2df4fca
fixed channel versions and rename variables
Daniel-VM Aug 29, 2024
cb0c18d
align spaces
Daniel-VM Oct 15, 2024
890f44c
fix bakta running only for one sample
Daniel-VM Oct 24, 2024
9e622f1
add changelog in #178
Daniel-VM Oct 24, 2024
10a7df8
include resequenced samples in test profile
Daniel-VM Oct 24, 2024
4ed19cb
remove view operator
Daniel-VM Oct 24, 2024
5a9559c
fix ambigous channel creation
Daniel-VM Oct 25, 2024
064996b
Merge pull request #178 from Daniel-VM/dev
Daniel-VM Oct 25, 2024
2bccce1
fixed matrix.test_name in linting
Daniel-VM Oct 25, 2024
fd2b54e
remove parameter section in git ci
Daniel-VM Oct 25, 2024
efe6309
Merge pull request #158 from Daniel-VM/concatenate_fasqs
Daniel-VM Oct 25, 2024
85bdf85
implement missing features in memory set up from nf-core tools 3.0.2
Daniel-VM Oct 25, 2024
aa42f95
update changelog #179
Daniel-VM Oct 25, 2024
02bf3dd
Merge pull request #179 from Daniel-VM/fix_linting_test_name
Daniel-VM Nov 5, 2024
8434c60
bump version 2.4.0
Daniel-VM Oct 24, 2024
f1809ce
update changelog #180
Daniel-VM Oct 25, 2024
9c95fb7
fix release date in #180
Daniel-VM Nov 5, 2024
067fb0f
Merge pull request #180 from Daniel-VM/bump-version-2.4.0
Daniel-VM Nov 5, 2024
262f741
uncomment required line for linting in --release mode
Daniel-VM Nov 5, 2024
e241ff8
update changelog in #182
Daniel-VM Nov 5, 2024
c476f50
Merge pull request #182 from Daniel-VM/dev
Daniel-VM Nov 6, 2024
ad68b1f
fix dfast conda issue by updating version
Daniel-VM Nov 6, 2024
0f7646a
update changelog in #183
Daniel-VM Nov 6, 2024
fc52c3e
Merge pull request #183 from Daniel-VM/dev
Daniel-VM Nov 6, 2024
bf367e4
added code review from #181
Daniel-VM Nov 18, 2024
cd1bf3e
fix linting in #184
Daniel-VM Nov 18, 2024
72cfd85
Merge pull request #184 from Daniel-VM/dev
Daniel-VM Nov 18, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#182](https://github.com/nf-core/bacass/pull/182) Uncommented required line to pass linting test in `--release` mode.
- [#179](https://github.com/nf-core/bacass/pull/179) Fixed matrix.test_name in linting and missing features from template 3.0.2.
- [#178](https://github.com/nf-core/bacass/pull/178) Fixed bakta running only for one sample.
- [#169](https://github.com/nf-core/bacass/pull/169) Fixed long reads polishing input channel.
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa

// Load nf-core/bacass custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bacass.config" : "/dev/null"
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bacass.config" : "/dev/null"

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
Expand Down
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