Run FastqScreen with subsampled data if available#120

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pontushojer wants to merge 96 commits into

nf-core:devfrom

pontushojer:ch_sampled

Commits on Jul 9, 2025

run fastqscreen with subsampled data
pontushojer
committed

Commits on Oct 7, 2025

Commits on Nov 24, 2025

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
Remove skip condition for samtools_index when calling picard_collectmultiplemetrics.
beatrizsavinhas
committed
lint errors
ramprasadn
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Remove outdated qc_bam.nf.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
Change if order in qc_bam.
beatrizsavinhas
committed
Added subworkflow prepare_genome
agrima2010
committed
Move creation of ch_hsmetrics_in to qc_bam.
beatrizsavinhas
committed
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 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
Merge branch 'dev' into ch_sampled
kjellinjonas
authored
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
Merge branch 'dev' into collethsmetrics
beatrizsavinhas
authored
Update README.md
beatrizsavinhas
authored
Updated CHANGE LOG
agrima2010
authored
Merge branch 'subworkflows' of https://github.com/agrima2010/seqinspector into subworkflows
agrima2010
authored
Merge pull request #151 from agrima2010/subworkflows
agrima2010
authored
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
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
Update snapshot for QC_BAM.
beatrizsavinhas
committed
Update CHANGELOG.md
beatrizsavinhas
authored

Commits on Dec 1, 2025

Add checks for empty params bait_intervals and target_intervals.
beatrizsavinhas
committed
Update usage.md
beatrizsavinhas
authored
Run prettier.
beatrizsavinhas
committed
Update PREPARE_GENOME input parameters description
beatrizsavinhas
committed
Merge pull request #159 from eliottBo/collecthsmetrics
beatrizsavinhas
authored

Commits on Dec 3, 2025

run fastqscreen with subsampled data
pontushojer
committed

Commits on Dec 4, 2025