Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests#9521

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kornkv wants to merge 90 commits intomasterfrom

fastq_remove_adapters_and_merge

Commits on Dec 8, 2025

Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests
kornkv
committed
Add ontologies to tcoffee/regressive and upp/align modules (#9484)

mirpedrol
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vagkaratzas
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Add module PBMARKDUP (#9457)

sainsachiko
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vagkaratzas
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Enable complex contrast strings in DESeq2 (#9473)

delfiterradas
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vagkaratzas
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Declare deepvariant optional html output (#9469)

authored and
vagkaratzas
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utils_nfcore_pipeline: fix small lang server error (#9492)

matthdsm
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vagkaratzas
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Fix hisat2/align to support large genome indices (.ht2l) (#9493)

authored and
vagkaratzas
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Update shinyngs modules to latest release (#9488)

delfiterradas
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vagkaratzas
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Update semibin/singleeasybin environment (#9495)

dialvarezs
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vagkaratzas
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add new ontology term to tcoffee align (#9497)

mirpedrol
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vagkaratzas
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tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (#9489)

authored and
vagkaratzas
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Sambamba depth add region bed input (#9498)

authored and
vagkaratzas
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fix fasta_index_methylseq and fastq_align_dedup workflows (#9496)

sateeshperi
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vagkaratzas
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Update test files for Glimpse (#9467)

authored and
vagkaratzas
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meta.yml schema: add `containers` section, fix order and simplify (#9503)

mashehu
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vagkaratzas
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update and add topics to snakemake module (#9454)

authored and
vagkaratzas
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fix sambamba depth stub version (#9509)

fellen31
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vagkaratzas
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anota2seq: wrong variable name for batch assignment (#9511)

suhrig
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vagkaratzas
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fix(anota2seq): add gene IDs and handle empty results (#9510)

authored and
vagkaratzas
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fix(decoupler): reorder imports and ensure environment variables are … (#9516)

atrigila
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vagkaratzas
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Add strdrop/build (#9512)

fellen31
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vagkaratzas
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chore(deps): update infrastructural dependencies

renovate[bot]
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vagkaratzas
committed
🔧 update image and bioconda container for VueGen to latest version (#9201)

authored and
vagkaratzas
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qsv/cat: bump version (#9518)

dialvarezs
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vagkaratzas
committed
Update haplogrep3 recipe to use topics (#9523)

authored and
vagkaratzas
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semibin/singleeasybin: bump version + migrate to topics (#9517)

authored and
vagkaratzas
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remove unused folder
vagkaratzas
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rename
vagkaratzas
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Merge branch 'master' into fastq_remove_adapters_and_merge
vagkaratzas
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trimmomatic revisit
vagkaratzas
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cutadapt revisit
vagkaratzas
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trimgalore revisit
vagkaratzas
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bbduk revisit
vagkaratzas
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fastp revisit
vagkaratzas
committed

Commits on Dec 12, 2025

New module: clusty (#9533)

Joon-Klaps
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vagkaratzas
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Bump TRGT to 4.1.0 (#9514)

authored and
vagkaratzas
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fix missing quotes (#9535)

mashehu
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vagkaratzas
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Fix dream to show more than 10 results (#9507)

authored and
vagkaratzas
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rename to more appropriate fastq_preprocess_seqkit (#9537)
vagkaratzas
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New module - TD2 (added modules for td2.longorfs & td2.predict) (#9475)

authored and
vagkaratzas
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Bump ichorCNA package build in ichorcna/createpon and ichorcna/run (#9531)

lbeltrame
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vagkaratzas
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RSeQC split_bam.py module implementation (#9536)

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vagkaratzas
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remove topics from multiqc (#9530)

nvnieuwk
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vagkaratzas
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bump to MultiQC version 1.33 (#9538)

authored and
vagkaratzas
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Add strdrop/call (#9513)

fellen31
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vagkaratzas
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Bump TRGT to 5.0.0 (#9541)

fellen31
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vagkaratzas
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Channel -> channel in some subwfs (#9542)

nvnieuwk
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vagkaratzas
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Migrate cat/fastq to topic channel (#9543)

Aratz
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vagkaratzas
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Add module picard/collectvariantcallingmetrics (#9502)

authored and
vagkaratzas
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fix tabix/tabix stub (#9544)

nvnieuwk
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vagkaratzas
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Unify msa modules (#9539)

authored and
vagkaratzas
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Fix missing version from subworkflow snapshot (#9548)

Aratz
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vagkaratzas
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New module: whatshap/phase (#9431)

authored and
vagkaratzas
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Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (#9549)

Joon-Klaps
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vagkaratzas
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plastid metagene_generate, make_wiggle, psite (#9482)

authored and
vagkaratzas
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Add index and threads to trgt/merge (#9545)

fellen31
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vagkaratzas
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Fix test path modification (#9465)

authored and
vagkaratzas
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Update xenium ranger modules and subworkflows (#9525)

authored and
vagkaratzas
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Version update: Modkit repair, callmods and bedmethyltobigwig (#9547)

authored and
vagkaratzas
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Update `GLIMPSE` sbwf (#9524)

authored and
vagkaratzas
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Add quilt imputation subworkflow (#9443)

LouisLeNezet
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vagkaratzas
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Update glimpse2 imputation subworkflow (#9434)

authored and
vagkaratzas
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Add `BEAGLE5` imputation subworkflow (#9550)

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vagkaratzas
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Add minimac4 imputation subworkfllow (#9451)

LouisLeNezet
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vagkaratzas
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Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow (#9559)

authored and
vagkaratzas
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Update cutadapt (#9551)
vagkaratzas
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Merge branch 'master' into fastq_remove_adapters_and_merge
vagkaratzas
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added cutadapt to stub now that stub gz is properly created, and removed cutadapt versions, since it is now ported to topics
vagkaratzas
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single-end test with tool skips
vagkaratzas
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Commits on Dec 15, 2025

Standarize and alignment for all imputation and alignment modules (#9566)

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vagkaratzas
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Update Infrastructural dependencies

renovate[bot]
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vagkaratzas
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Remove .view() (#9567)

LouisLeNezet
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vagkaratzas
committed
Bump strdrop to 0.3.1 (#9565)

fellen31
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vagkaratzas
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Remove unecessary tags (#9568)

LouisLeNezet
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vagkaratzas
committed
Update trimgalore (#9570)

committed
trimgalore output versions removed
vagkaratzas
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Merge branch 'master' into fastq_remove_adapters_and_merge
vagkaratzas
authored

Commits on Dec 16, 2025