nf-core/seqinspector

Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.

genomicsquality-control

Launch version 1.1.0 https://github.com/nf-core/seqinspector

Version history

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What’s Changed

Back to dev by @maxulysse in https://github.com/nf-core/seqinspector/pull/191
FEAT: Refactor tools selection by @maxulysse in https://github.com/nf-core/seqinspector/pull/192
Docs update by @FranBonath in https://github.com/nf-core/seqinspector/pull/205
FEAT: add –fai option by @maxulysse in https://github.com/nf-core/seqinspector/pull/202
Adds FASTQE for summarising FASTQ scores as emojis by @maxulysse in https://github.com/nf-core/seqinspector/pull/206
Added Fastp module by @agrima2010 in https://github.com/nf-core/seqinspector/pull/204
Adds fq/lint for early validation of FASTQs by @agrima2010 in https://github.com/nf-core/seqinspector/pull/208
remove sort_bam params by @maxulysse in https://github.com/nf-core/seqinspector/pull/213
Add support for ToulligQC for long read support by @TMAdams in https://github.com/nf-core/seqinspector/pull/109
Add kraken2 phylogenetic assignment subworkflow by @agrima2010 in https://github.com/nf-core/seqinspector/pull/210
FEAT: update all modules by @maxulysse in https://github.com/nf-core/seqinspector/pull/215
FEAT: Add CheckQC by @matrulda in https://github.com/nf-core/seqinspector/pull/212
FEAT: Add MultiQCSAV support by @nkongenelly in https://github.com/nf-core/seqinspector/pull/209
FEAT: Refactor by @maxulysse in https://github.com/nf-core/seqinspector/pull/216
fix subworkflow name + add tests + use subsampling by @maxulysse in https://github.com/nf-core/seqinspector/pull/218
FEAT: workflow output for multiqc by @maxulysse in https://github.com/nf-core/seqinspector/pull/220
WIP - workflow output by @maxulysse in https://github.com/nf-core/seqinspector/pull/221
Finishing workflow output for all reports by @maxulysse in https://github.com/nf-core/seqinspector/pull/222
FEAT: All pipeline is now using workflow outputs + update docs by @maxulysse in https://github.com/nf-core/seqinspector/pull/223
Fix issues with workflow output and edge release by @maxulysse in https://github.com/nf-core/seqinspector/pull/224
Add sequali by @pontushojer in https://github.com/nf-core/seqinspector/pull/134
Enable custom tools selection from command line by @pontushojer in https://github.com/nf-core/seqinspector/pull/227
FEAT: add stub tests by @maxulysse in https://github.com/nf-core/seqinspector/pull/226
update all modules/subworkflows by @maxulysse in https://github.com/nf-core/seqinspector/pull/228
Important! Template update for nf-core/tools v4.0.1 by @nf-core-bot in https://github.com/nf-core/seqinspector/pull/232
Important! Template update for nf-core/tools v4.0.2 by @nf-core-bot in https://github.com/nf-core/seqinspector/pull/233
Add pipeline-level PICARD tests by @maxulysse in https://github.com/nf-core/seqinspector/pull/234
update MultiQC and other dependencies by @maxulysse in https://github.com/nf-core/seqinspector/pull/235
Feat: add Seqkit by @sarahjeeeze in https://github.com/nf-core/seqinspector/pull/59
FEAT: Improve citation system to dynamically build tool citations by @maxulysse in https://github.com/nf-core/seqinspector/pull/237
Fix tool bundles documentation to match code by @maxulysse in https://github.com/nf-core/seqinspector/pull/239
Fix FASTQE default tool marking in README by @maxulysse in https://github.com/nf-core/seqinspector/pull/240
Fix Python/PyYAML case mismatch in toolReferencesMap by @maxulysse in https://github.com/nf-core/seqinspector/pull/238
Feat: add bbmap/clumpify by @maxulysse in https://github.com/nf-core/seqinspector/pull/236
corrected the pipeline introduction tool list for fq lint by @agrima2010 in https://github.com/nf-core/seqinspector/pull/244
feat: smart subsampling with –subsample_tools by @maxulysse in https://github.com/nf-core/seqinspector/pull/243
fix repeated tool in usage docs by @pontushojer in https://github.com/nf-core/seqinspector/pull/245
Add riker module for BAM-level QC metrics by @maxulysse in https://github.com/nf-core/seqinspector/pull/246
Add AGENTS.md file with nf-core agent instructions by @maxulysse in https://github.com/nf-core/seqinspector/pull/247
Update modules by @maxulysse in https://github.com/nf-core/seqinspector/pull/249
Prepare release 1.1.0 by @maxulysse in https://github.com/nf-core/seqinspector/pull/250
Skip conda tests for CheckQC by @maxulysse in https://github.com/nf-core/seqinspector/pull/252
Update metro map by @maxulysse in https://github.com/nf-core/seqinspector/pull/225
Address review comments for 1.1.0 release by @maxulysse in https://github.com/nf-core/seqinspector/pull/253
Fix rundirparser test snapshots by @maxulysse in https://github.com/nf-core/seqinspector/pull/255
Address review comments from PR #251 by @maxulysse in https://github.com/nf-core/seqinspector/pull/256
Standardize output docs layout by @maxulysse in https://github.com/nf-core/seqinspector/pull/258
Release 1.1.0 - Veronica Mars by @maxulysse in https://github.com/nf-core/seqinspector/pull/251

New Contributors

@TMAdams made their first contribution in https://github.com/nf-core/seqinspector/pull/109
@sarahjeeeze made their first contribution in https://github.com/nf-core/seqinspector/pull/59

Full Changelog: https://github.com/nf-core/seqinspector/compare/1.0.1...1.1.0

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What’s Changed

Zenodo by @maxulysse in https://github.com/nf-core/seqinspector/pull/180
Back to dev by @maxulysse in https://github.com/nf-core/seqinspector/pull/181
FIX: Remove diff for bwamem2/mem by @maxulysse in https://github.com/nf-core/seqinspector/pull/182
FIX: tag collision warning by @maxulysse in https://github.com/nf-core/seqinspector/pull/183
FIX: No fasta provided by @maxulysse in https://github.com/nf-core/seqinspector/pull/185
Add a TAG for MultiQC by @maxulysse in https://github.com/nf-core/seqinspector/pull/184
remove slack url report by @maxulysse in https://github.com/nf-core/seqinspector/pull/186
prepare release 1.0.1 by @maxulysse in https://github.com/nf-core/seqinspector/pull/187
Fix GHA by @maxulysse in https://github.com/nf-core/seqinspector/pull/189
FIX: GHA - indentation by @maxulysse in https://github.com/nf-core/seqinspector/pull/190
Release 1.0.1 by @maxulysse in https://github.com/nf-core/seqinspector/pull/188

Full Changelog: https://github.com/nf-core/seqinspector/compare/1.0.0...1.0.1

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Initial release of seqinspector

What’s Changed

Skip RUNDIRPARSER if no rundir information is available by @matrulda in https://github.com/nf-core/seqinspector/pull/167
Address review comments by @maxulysse in https://github.com/nf-core/seqinspector/pull/168
prepare release 1.0.0 by @maxulysse in https://github.com/nf-core/seqinspector/pull/169
rescure size from the pipeline tests by @maxulysse in https://github.com/nf-core/seqinspector/pull/171
fix conda env for rundirparser by @maxulysse in https://github.com/nf-core/seqinspector/pull/172
addess review comments by @maxulysse in https://github.com/nf-core/seqinspector/pull/173
Minor code polish by @maxulysse in https://github.com/nf-core/seqinspector/pull/174
Update all modules and subworkflows + migrate to topics versions by @maxulysse in https://github.com/nf-core/seqinspector/pull/175
FIX: No modules binaries by @maxulysse in https://github.com/nf-core/seqinspector/pull/176
Remove unused modules (bowtie2/build, fastqscreen/buildfromindex) by @maxulysse in https://github.com/nf-core/seqinspector/pull/177
Fix schema and docs by @maxulysse in https://github.com/nf-core/seqinspector/pull/178
Update minimal Nextflow version by @maxulysse in https://github.com/nf-core/seqinspector/pull/179
Release 1.0.0 by @maxulysse in https://github.com/nf-core/seqinspector/pull/170

Full Changelog: https://github.com/nf-core/seqinspector/commits/1.0.0