31 Pull requests merged by 17 people

• Replace ubuntu for all modules using it - meta PR

  #7215 merged Dec 13, 2024

• Fix conda pytests cf #7215

  #7219 merged Dec 13, 2024

• fix vcf2db: add missing dependencies

  #7217 merged Dec 13, 2024

• Changed paths of files used in main.nf.test from test-data/methylseq …

  #7212 merged Dec 13, 2024

• Update nf-test.config

  #7214 merged Dec 13, 2024

• rm test resourceLimits

  #7213 merged Dec 13, 2024

• use detailed profiles in tests/nf-test.config

  #7207 merged Dec 13, 2024

• Fix subworkflow imports for bam_dedup_umi

  #7209 merged Dec 12, 2024

• Generic UMI handling subworkflow

  #7208 merged Dec 12, 2024

• Make busco/busco seq_dir output optional

  #7203 merged Dec 12, 2024

• Update BUSCO module

  #7199 merged Dec 11, 2024

• Update ampcombi 2.0.1

  #7142 merged Dec 11, 2024

• Facilitate iteration in differential subworkflow

  #7115 merged Dec 11, 2024

• Correct non-gzipped output from clustalo/align

  #7197 merged Dec 11, 2024

• update module propr/grea

  #7198 merged Dec 11, 2024

• update parabricks/applybqsr

  #7189 merged Dec 11, 2024

• Modify DAS_Tool input structure, bump version, switch to nf-test

  #7163 merged Dec 11, 2024

• Port parabricks/dbsnp to nf-test

  #6977 merged Dec 11, 2024

• port parabricks/indexgvcf to nf-test

  #6996 merged Dec 11, 2024

• METABAT2_METABAT2: Add nf-test and stub

  #7196 merged Dec 11, 2024

• new module pangolin/updatedata & patch pangolin/run

  #7182 merged Dec 10, 2024

• bump ngsbits

  #7193 merged Dec 10, 2024

• Fix ci confirm pass

  #7186 merged Dec 10, 2024

• MEGAHIT: fix single-end input

  #7190 merged Dec 10, 2024

• Add foldmason msa2lddtreport

  #7191 merged Dec 10, 2024

• add stub test for samtools/mpileup

  #7192 merged Dec 10, 2024

• Update: deseq2/differential for upcoming improved standardisation of template modules

  #7178 merged Dec 10, 2024

• Add foldmason createdb

  #7180 merged Dec 10, 2024

• Update GitHub Actions

  #7126 merged Dec 10, 2024

• port parabricks/genotypegvcf to nf-test

  #6980 merged Dec 10, 2024

• add TCOFFEE/EXTRACTFROMPDB

  #7167 merged Dec 9, 2024

16 Pull requests opened by 12 people

• Fix abritamr/run

  #7176 opened Dec 7, 2024

• Fix minor typos

  #7177 opened Dec 8, 2024

• Add wipertools module (#7184)

  #7185 opened Dec 9, 2024

• bump star build

  #7194 opened Dec 10, 2024

• Add nftests custom modules

  #7201 opened Dec 11, 2024

• Update vcf2maf and add stub tests

  #7202 opened Dec 11, 2024

• Update CENTRIFUGE: bump versions, fix missing args, and command formatting

  #7205 opened Dec 12, 2024

• Update file naming strategy

  #7206 opened Dec 12, 2024

• Add busco downloads as output

  #7210 opened Dec 12, 2024

• Remove `compressed` flag from all mmseqs modules

  #7211 opened Dec 12, 2024

• DUMMY DELETE ME: Test if UNTAR fails on self_hosted runners

  #7216 opened Dec 13, 2024

• Add module custom_tabulargseatochip

  #7218 opened Dec 13, 2024

• Add propd to abundance_differential_filter subworkflow

  #7220 opened Dec 13, 2024

• split out gunzip from #7215

  #7221 opened Dec 13, 2024

• Split untar out from #7215

  #7222 opened Dec 13, 2024

• Move Changes action locally

  #7223 opened Dec 13, 2024

6 Issues closed by 4 people

• [FEATURE] Centralize all modules using ubuntu container into a single container

  #5968 closed Dec 13, 2024

• Environment.ymls using seqera containers fail linting

  #5813 closed Dec 11, 2024

• Update GREA

  #7195 closed Dec 11, 2024

• new module: foldmason/msa2lddtreport

  #7181 closed Dec 10, 2024

• new module: foldmason/createdb

  #7179 closed Dec 10, 2024

• new module: tcoffee/extractfrompdb

  #7166 closed Dec 9, 2024

5 Issues opened by 5 people

• new module: VueGen

  #7204 opened Dec 12, 2024

• Add `TABULAR_TO_GSEA_CHIP` to nf-core/modules

  #7200 opened Dec 11, 2024

• new module: AGAT/SPFILTERBYORFSIZE

  #7187 opened Dec 10, 2024

• new module: WIPERTOOLS

  #7184 opened Dec 9, 2024

• bbmap/bbduk sometimes fails to create the versions.yml file

  #7183 opened Dec 9, 2024

44 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• Add PASTA

  #6095 commented on Dec 10, 2024 • 17 new comments

• Add sylph/profile module

  #7118 commented on Dec 11, 2024 • 7 new comments

• add module for btyper3

  #3817 commented on Dec 10, 2024 • 7 new comments

• port parabricks/mutectcaller to nf-test

  #6991 commented on Dec 11, 2024 • 2 new comments

• Add sam2lca/updadb module

  #7059 commented on Dec 11, 2024 • 2 new comments

• port parabricks/deepvariant to nf-test

  #6995 commented on Dec 11, 2024 • 2 new comments

• update bowtie2 v2.5.4

  #6870 commented on Dec 11, 2024 • 1 new comment

• Update toulligqc to 2.7.1

  #6786 commented on Dec 10, 2024 • 1 new comment

• Proovframe update

  #7158 commented on Dec 13, 2024 • 1 new comment

• Add missing file input to bcftools/annotate

  #6942 commented on Dec 10, 2024 • 1 new comment

• ci: Update module_name filter step

  #7106 commented on Dec 13, 2024 • 1 new comment

• Add stimulus transform

  #6886 commented on Dec 13, 2024 • 0 new comments

• Remove langage server warnings

  #6937 commented on Dec 13, 2024 • 0 new comments

• Parabricks haplotypecaller version update and tests migrated to nf-test

  #6976 commented on Dec 10, 2024 • 0 new comments

• Update bclconvert

  #7034 commented on Dec 13, 2024 • 0 new comments

• Update bowtie2 align test

  #7038 commented on Dec 13, 2024 • 0 new comments

• Update decoupler

  #7068 commented on Dec 11, 2024 • 0 new comments

• ci: Let wave fail

  #7101 commented on Dec 13, 2024 • 0 new comments

• Update main.nf

  #7120 commented on Dec 13, 2024 • 0 new comments

• Update biocontainers/abritamr Docker tag to v1.0.19

  #7130 commented on Dec 10, 2024 • 0 new comments

• Add HOMER Uniqmap tests

  #7143 commented on Dec 8, 2024 • 0 new comments

• Bcl2fastq bump

  #7161 commented on Dec 7, 2024 • 0 new comments

• Update DeepVariant

  #7171 commented on Dec 11, 2024 • 0 new comments

• Fix cellranger multi handling of crispr data

  #7175 commented on Dec 11, 2024 • 0 new comments

• new module: Baysor

  #5125 commented on Dec 10, 2024 • 0 new comments

• pip field in environment.yml fails linting

  #5814 commented on Dec 11, 2024 • 0 new comments

• [FEATURE] Build automation for fetching Seqera Containers

  #6694 commented on Dec 11, 2024 • 0 new comments

• Migrate modules to Seqera Containers

  #5832 commented on Dec 11, 2024 • 0 new comments

• Renovate Workflow

  #4306 commented on Dec 11, 2024 • 0 new comments

• Use of OCI Containers

  #4519 commented on Dec 11, 2024 • 0 new comments

• Bulk update modules to use Seqera Containers

  #6698 commented on Dec 11, 2024 • 0 new comments

• Add renovate comments to environment.yml

  #6504 commented on Dec 11, 2024 • 0 new comments

• Use Conda lock files

  #5835 commented on Dec 11, 2024 • 0 new comments

• new module: Phylophlan

  #959 commented on Dec 11, 2024 • 0 new comments

• Renovate Dashboard 🤖

  #4211 commented on Dec 13, 2024 • 0 new comments

• Subworkflow - PON creation - Handle intervals + refactor

  #3675 commented on Dec 13, 2024 • 0 new comments

• Add nf-test for fastq_trim_fastp_fastqc subworkflow

  #3809 commented on Dec 13, 2024 • 0 new comments

• Update mageck modules

  #4358 commented on Dec 11, 2024 • 0 new comments

• remove renovate-config-validator updates

  #5737 commented on Dec 13, 2024 • 0 new comments

• Add dshbio/fastatoparquet module

  #5994 commented on Dec 11, 2024 • 0 new comments

• Add Seurat/MULTI-seq

  #6168 commented on Dec 9, 2024 • 0 new comments

• Script to fetch unique conda environments

  #6659 commented on Dec 11, 2024 • 0 new comments

• Fixed linked site location for bbam tools

  #6768 commented on Dec 11, 2024 • 0 new comments

• DON'T MERGE: Bump sortmerna

  #6814 commented on Dec 13, 2024 • 0 new comments