Release 1.0.0#170

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maxulysse wants to merge 638 commits intomasterfrom

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Commits on Nov 18, 2025

.bai files in the same folder as bam files
agrima2010
authored

Commits on Nov 20, 2025

Commits on Nov 24, 2025

Merge branch 'dev' into run-dirs
matrulda
authored
Update rundirparser test and add nextflow config for it
matrulda
committed
Fix #94. Remove outdated TODOs
KarNair
committed
Add #94 to Changelog
KarNair
committed
Add #94 to Changelog
KarNair
committed
Update README.md

FranBonath
and
pontushojer
authored
Merge branch 'dev' into dev_docs
FranBonath
authored
Merge pull request #145 from KarNair/validate-test-data
KarNair
authored
Merge pull request #111 from Patricie34/dev_docs
FranBonath
authored
add tubemap and logo to intro page
FranBonath
committed
fix merge conflicts
FranBonath
committed
update tubemap and some updates to README
FranBonath
committed
update tubmap again
FranBonath
committed
add SeqFu Stats to README.md
FranBonath
committed
Install picard_collecthsmetrics.
beatrizsavinhas
committed
Install picard_createsequencedictionary.
beatrizsavinhas
committed
Add test samplesheet and test config.
beatrizsavinhas
committed
Change modules.json to include installed modules.
beatrizsavinhas
committed
Set up input parameters.
beatrizsavinhas
committed
Add picard_collecthsmetrics to workflow.
beatrizsavinhas
committed
Make SAMTOOLS_INDEX required if bwamem2_mem is run.
beatrizsavinhas
committed
Rundirparser: Add tar support, remove dummy script, update format of illumina mqc file
matrulda
committed
Remove skip condition for samtools_index when calling picard_collectmultiplemetrics.
beatrizsavinhas
committed
Have tools list in README in Table
FranBonath
committed
lint errors
ramprasadn
committed
add darkmode options in README, add darkmode tubemap
FranBonath
committed
lint warnings
ramprasadn
committed
Add qc_bam subworkflow to run picard_collecthsmetrics.
beatrizsavinhas
committed
Add subworkflow qc_bam.
beatrizsavinhas
committed
Add subworkflow QC_BAM.
beatrizsavinhas
committed
Add logic to skip collecthsmetrics by default through addin "run_picard_collecthsmetrics" flag.
beatrizsavinhas
committed
Modified seqinspector.nf and added subworkflow
agrima2010
committed

Commits on Nov 25, 2025

Add TMP_DIR argument to picard_collecthsmetrics.
beatrizsavinhas
committed
update README and usage.md
FranBonath
committed
Create subworkflow directory. Change channels created from params to seqcinspector.nf instead of subworkflow.
beatrizsavinhas
committed
Add curly braket.
beatrizsavinhas
committed
Add second sample to samplesheet.
beatrizsavinhas
committed
Fix ch_ref_dict.
beatrizsavinhas
committed
Remove outdated qc_bam.nf.
beatrizsavinhas
committed
Update README.md

FranBonath
and
MatthiasZepper
authored
Update README.md

FranBonath
and
MatthiasZepper
authored
[automated] Fix code linting
nf-core-bot
committed
Change if order in qc_bam.
beatrizsavinhas
committed
Merge pull request #148 from FranBonath/dev
FranBonath
authored
update output.md
FranBonath
committed
Added subworkflow prepare_genome
agrima2010
committed
Move creation of ch_hsmetrics_in to qc_bam.
beatrizsavinhas
committed
Merge branch 'nf-core:dev' into output_changes
FranBonath
authored
Add qc_bam test!
beatrizsavinhas
committed
Remove test config and samplesheet.
beatrizsavinhas
committed
Minor changes
agrima2010
committed
Snapshots
agrima2010
committed
Add defaults for collecthsmetrics in modules.config.
beatrizsavinhas
committed
Fix so output files are only accessed if QC_BAM is run.
beatrizsavinhas
committed
ss
agrima2010
authored
fix precommit
agrima2010
authored
Merge branch 'dev' into collethsmetrics
eliottBo
committed
Add rundirparser as skip option
matrulda
committed
Adapt tests for rundirparser (only NovaSeq6000 test data have the required file for the test)
matrulda
committed
Add information about run_picard_collecthsmetrics flag to usage.md
eliottBo
committed
Changed parameter bwa_index to bwamem2 and changed channel names
agrima2010
authored
Update README.md
beatrizsavinhas
committed
Update CITATIONS.md.
beatrizsavinhas
committed
Add PR link to CHANGELOG.md
eliottBo
committed
Merge branch 'collethsmetrics' of https://github.com/eliottBo/seqinspector into collethsmetrics
eliottBo
committed
Update output.md.
beatrizsavinhas
committed
WIP: Updating module test for rundirparser
matrulda
committed
Remove cg_test profile.
beatrizsavinhas
committed
Add output file description for CollectHsMetrics in output.md
eliottBo
committed
update tools table in README
FranBonath
committed
Fix title in Picard CollectHSmetrics in output.md
eliottBo
committed
Add File description for collecthsmetrics in output.md
eliottBo
committed
Merge branch 'collethsmetrics' of https://github.com/eliottBo/seqinspector into collethsmetrics
eliottBo
committed
Merge branch 'dev' into changes_usage.md
KarNair
authored
Merge pull request #150 from ramprasadn/pipeline-lint
ramprasadn
authored
Update README.md

FranBonath
and
KarNair
authored
[automated] Fix code linting
nf-core-bot
committed
Added params in root main.nf and snapshots
agrima2010
authored
Merge branch 'dev' into subworkflows
agrima2010
authored
Merge pull request #153 from FranBonath/changes_usage.md
KarNair
authored
Move picard_collectmultiplemetrics to QC_BAM.
beatrizsavinhas
committed
Merge branch 'dev' into collethsmetrics
beatrizsavinhas
authored
Update README.md
beatrizsavinhas
authored
Fix output channels.
beatrizsavinhas
committed
Updated CHANGE LOG
agrima2010
authored
Merge branch 'dev' into change-qc-bam
beatrizsavinhas
authored
Merge branch 'subworkflows' of https://github.com/agrima2010/seqinspector into subworkflows
agrima2010
authored
Merge pull request #151 from agrima2010/subworkflows
agrima2010
authored
Fix linting issues.
beatrizsavinhas
committed
Update CHANGELOG.md
beatrizsavinhas
authored
Merge branch 'dev' into collecthsmetrics
beatrizsavinhas
authored
Update seqinspector.nf
beatrizsavinhas
committed
Fix linting erros.
beatrizsavinhas
committed
Fix test snap generation.
beatrizsavinhas
committed

Commits on Nov 26, 2025

Fix linting issues.
beatrizsavinhas
committed
Run prettier and remove trailing whitespace.
beatrizsavinhas
committed
Fix end of files.
beatrizsavinhas
committed
Remove cg_test config.
beatrizsavinhas
committed
Trim trailing whitespace.
beatrizsavinhas
committed
Remove picard_collecthsmetrics from skip_tools as it is not run by default.
beatrizsavinhas
committed
Update usage.md.
beatrizsavinhas
committed
Seqtk add relative sample sets and warning

committed
Fixing tests
nkongenelly
committed
Fixed test error
nkongenelly
committed
[automated] Fix code linting
nf-core-bot
committed
Harshil alignment
eliottBo
committed
Update ro-crate
eliottBo
committed

Commits on Nov 27, 2025

Format seqinspector.nf.
beatrizsavinhas
committed
Restore output.md.
beatrizsavinhas
committed
Add input parameter notes for QC_BAM.
beatrizsavinhas
committed
Fix input notes.
beatrizsavinhas
committed
Update input parameter notes.
beatrizsavinhas
committed
Move PICARD_CREATESEQUENCEDICTIONARY to PREPARE_GENOME. Adjust QC_BAM tests.
beatrizsavinhas
committed
Initialise ch_ref_dict in PREPARE_GENOME.
beatrizsavinhas
committed

Commits on Nov 28, 2025

Harshil alignment
eliottBo
committed
Merge branch 'dev' into multiqc-index
pontushojer
authored
Update snapshot for QC_BAM.
beatrizsavinhas
committed
Update CHANGELOG.md
beatrizsavinhas
authored
Merge branch 'collecthsmetrics' into change-qc-bam
beatrizsavinhas
committed
Correct QC_BAM main.nf.
beatrizsavinhas
committed

Commits on Dec 1, 2025

Remove PICARD_COLLECTMULTIPLEMETRICS from seqinspector.nf.
beatrizsavinhas
committed
Fix linting issues.
beatrizsavinhas
committed
Add checks for empty params bait_intervals and target_intervals.
beatrizsavinhas
committed
Fix QC_BAM input parameters.
beatrizsavinhas
committed
Update QC_BAM test.
beatrizsavinhas
committed
Update usage.md
beatrizsavinhas
authored
Merge branch 'collecthsmetrics' into change-qc-bam
beatrizsavinhas
committed
Edit CHANGELOG.md
beatrizsavinhas
committed
Run prettier.
beatrizsavinhas
committed
Merge branch 'collecthsmetrics' into change-qc-bam
beatrizsavinhas
committed
Rename ch_reference_fai.
beatrizsavinhas
committed
Update PREPARE_GENOME input parameters description
beatrizsavinhas
committed
Merge pull request #159 from eliottBo/collecthsmetrics
beatrizsavinhas
authored
Merge branch 'nf-core:dev' into change-qc-bam
beatrizsavinhas
authored

Commits on Dec 2, 2025

Fix prepare_genome/main.nf
beatrizsavinhas
committed
Add tests
beatrizsavinhas
committed
Update test
beatrizsavinhas
committed
Merge branch 'dev' into test-prepare-genome
beatrizsavinhas
authored
Update prepare_genome/main.nf
beatrizsavinhas
committed
Add publishDir for PICARD_CREATESEQUENCEDICTIONARY
beatrizsavinhas
committed
Refactor tests
beatrizsavinhas
committed
Fix end of file main.nf.test
beatrizsavinhas
committed
Update CHANGELOG.md
beatrizsavinhas
committed
Update CHANGELOG.md
beatrizsavinhas
committed
Revert redundant changes in modules.config
beatrizsavinhas
committed
Update some snapshots
beatrizsavinhas
committed
More snapshot updates
beatrizsavinhas
committed
Update remaining snapshot
beatrizsavinhas
committed
Re-add changes to modules.config
beatrizsavinhas
committed
Small changes in comments in main.nf.test
beatrizsavinhas
committed
Small changes in comments in main.nf.test
beatrizsavinhas
committed
Add nextflow.config to tests
beatrizsavinhas
committed
Update tests and snapshot
beatrizsavinhas
committed
Add EOL to nextflow.config
beatrizsavinhas
committed

Commits on Dec 3, 2025

Update QC_BAM input description
beatrizsavinhas
committed
Update PREPARE_GENOME test configs
beatrizsavinhas
committed
Update snapshots
beatrizsavinhas
committed
Add test nextflow.config
beatrizsavinhas
committed
Update test configs to remove hardcoded pipelines_testdata_base_path and refer instead to the basic test/nextflow.config
beatrizsavinhas
committed
Remove redundant / in test-data paths
beatrizsavinhas
committed
Merge pull request #158 from eliottBo/change-qc-bam
beatrizsavinhas
authored
Merge branch 'nf-core:dev' into test-prepare-genome
beatrizsavinhas
authored

Commits on Dec 4, 2025

run fastqscreen with subsampled data if available
pontushojer
committed
update changelog
pontushojer
committed
Fix bug preventing picard_multiple_metrics files from being passed to multiqc_files
beatrizsavinhas
committed
Update CHANGELOG.md
beatrizsavinhas
committed

Commits on Dec 5, 2025

Update CHANGELOG.md
beatrizsavinhas
authored

Commits on Dec 8, 2025

Commits on Dec 9, 2025

Merge pull request #162 from beatrizsavinhas/test-prepare-genome
beatrizsavinhas
authored

Commits on Dec 10, 2025

Merge pull request #135 from pontushojer/multiqc-index
pontushojer
authored

Commits on Dec 11, 2025

Commits on Dec 12, 2025

Commits on Jan 19, 2026

Commits on Jan 20, 2026

Commits on Feb 6, 2026

Write warning if rundir is missing for a sample
matrulda
committed

Commits on Feb 9, 2026

Merge pull request #167 from matrulda/issue-166_document_rundir_parser
maxulysse
authored

Commits on Feb 10, 2026

Address review comments (#168)

maxulysse
and
pontushojer
authored

Commits on Feb 11, 2026

Commits on Feb 16, 2026

addess review comments (#173)
maxulysse
authored

Commits on Feb 19, 2026

Minor code polish (#174)
maxulysse
authored

Commits on Feb 20, 2026