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ctglab / ctgflow Public template

forked from tjbencomo/ngs-pipeline

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feat: depth reporting, multiQC, readme update, sparse fixing#11

Merged

danilotat merged 20 commits intomasterctglab/ctgflow:masterfrom

10-add-extensive-quality-control-on-alignmentctglab/ctgflow:10-add-extensive-quality-control-on-alignmentCopy head branch name to clipboard

Feb 23, 2026

Conversation Commits20 (20)Checks Files changed

Merged

feat: depth reporting, multiQC, readme update, sparse fixing#11
danilotat merged 20 commits intomasterfrom
10-add-extensive-quality-control-on-alignment

Commits

Commits on Feb 19, 2026

chore: unused files removal
danilotat
committed
feat: smaller conda envs
danilotat
committed
upd: lighter conda env in use
danilotat
committed
feat: samtools conda env
danilotat
committed
feat: integration of qc reports, smaller common, updated snakefile
danilotat
committed
upd: config update
danilotat
committed
feat: updated schema convention
danilotat
committed
ci: action update
danilotat
committed
doc: readme update
danilotat
committed
fix: bwa env
danilotat
committed
fix: revert to single gatk+bwa+samtools env
danilotat
committed
feat: mock units file
danilotat
committed
fix: sparse fixing, mutect using BAM
danilotat
committed
doc: readme update
danilotat
committed
fix: sparse fixing, mutect using BAM
danilotat
committed

Commits on Feb 20, 2026

chore: outfolder prefix via lambda
danilotat
committed
chore: outfolder prefix via lambda
danilotat
committed
fix: pinned version of multiqc
danilotat
committed
fix: pinned version of multiqc
danilotat
committed
fix: pinned version of multiqc
danilotat
committed

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