# nf-core/modules Issue Triage Report

**Date:** 2026-02-27
**Total open issues:** 474

## 1. Already Implemented - Close (11 issues)

| Issue | Requested | Exists at |
|-------|-----------|-----------|
| [#4372](https://github.com/nf-core/modules/issues/4372) | CellBender | `cellbender/removebackground`, `cellbender/merge` |
| [#5914](https://github.com/nf-core/modules/issues/5914) | PLINK2/extract | `plink2/extract` |
| [#6110](https://github.com/nf-core/modules/issues/6110) | mcstaging/phenoimager2mc | `mcstaging/phenoimager2mc` |
| [#6233](https://github.com/nf-core/modules/issues/6233) | vsearch/fastqfilter | `vsearch/fastqfilter` |
| [#6548](https://github.com/nf-core/modules/issues/6548) | shigapass | `shigapass` |
| [#7946](https://github.com/nf-core/modules/issues/7946) | plink2/het | `plink2/het` |
| [#8870](https://github.com/nf-core/modules/issues/8870) | slamdunk | `slamdunk/all`, `slamdunk/map` |
| [#8971](https://github.com/nf-core/modules/issues/8971) | crispresso2 | `crispresso2` |
| [#9013](https://github.com/nf-core/modules/issues/9013) | hificnv | `hificnv` |
| [#9075](https://github.com/nf-core/modules/issues/9075) | modkit/repair | `modkit/repair` |
| [#9140](https://github.com/nf-core/modules/issues/9140) | seqfu/check | `seqfu/check` |

## 2. Partially Implemented - Review before closing (5 issues)

| Issue | Requested | What exists | Gap |
|-------|-----------|-------------|-----|
| [#6115](https://github.com/nf-core/modules/issues/6115) | ASCAT/ASCAT_TUMOR_ONLY | `ascat` | Tumor-only mode may not be supported |
| [#9054](https://github.com/nf-core/modules/issues/9054) | opt (off-target-probe-tracker) | `opt/flip`, `opt/stat`, `opt/track` | Looks complete - verify with requester |
| [#9280](https://github.com/nf-core/modules/issues/9280) | pcgr | `pcgr/getref` only | Main `pcgr` module missing |
| [#9791](https://github.com/nf-core/modules/issues/9791) | CELLPOSE-SAM | `cellpose` | SAM variant is different from base cellpose |
| [#9887](https://github.com/nf-core/modules/issues/9887) | sentieon-cli/dnascope-longread | `sentieon/dnascope` | sentieon-cli wrapper + longread-specific version missing |

## 3. Tool Exists but Requested Subcommand Missing (4 issues)

| Issue | Requested | Available |
|-------|-----------|-----------|
| [#4499](https://github.com/nf-core/modules/issues/4499) | gridss/preprocess | `gridss/gridss`, `gridss/generateponbedpe`, `gridss/somaticfilter` |
| [#4502](https://github.com/nf-core/modules/issues/4502) | gridss/assembly | same as above |
| [#4503](https://github.com/nf-core/modules/issues/4503) | gridss/variantcall | same as above |
| [#8422](https://github.com/nf-core/modules/issues/8422) | gridss/annotate | same as above |

## 4. Already Labeled Stale (21 issues)

These already have the `stale` label. Batch-close if no response.

- [#4634](https://github.com/nf-core/modules/issues/4634) - new submodule: salmon quantmerge
- [#4662](https://github.com/nf-core/modules/issues/4662) - new module: Somatosim - simulate mutations in a bam file
- [#4793](https://github.com/nf-core/modules/issues/4793) - Add new module: Sanntis
- [#4808](https://github.com/nf-core/modules/issues/4808) - new module: delly/filter
- [#5333](https://github.com/nf-core/modules/issues/5333) - new module: decouplerPKN
- [#5334](https://github.com/nf-core/modules/issues/5334) - Create new module for cell phenotyping with MAPS
- [#6557](https://github.com/nf-core/modules/issues/6557) - new module: HMMER/TIDY
- [#6611](https://github.com/nf-core/modules/issues/6611) - new module: add microbial reference genomes to Sarek 
- [#6703](https://github.com/nf-core/modules/issues/6703) - new module: MICROSAM
- [#7527](https://github.com/nf-core/modules/issues/7527) - new module: ont/spectre
- [#7778](https://github.com/nf-core/modules/issues/7778) - new module: MATLOCK/BAM2JUICER
- [#7786](https://github.com/nf-core/modules/issues/7786) - new module: BEDTOOLS/RANDOM
- [#7970](https://github.com/nf-core/modules/issues/7970) - new module: modkit/motifsearch
- [#7975](https://github.com/nf-core/modules/issues/7975) - new module: GCTA/GSMR
- [#7990](https://github.com/nf-core/modules/issues/7990) - new module: protein-activity/viper
- [#8451](https://github.com/nf-core/modules/issues/8451) - new module: RTN/TNA
- [#8733](https://github.com/nf-core/modules/issues/8733) - new module: pvactools/pvacseq
- [#8734](https://github.com/nf-core/modules/issues/8734) - new module: pvactools/installvepplugin
- [#8750](https://github.com/nf-core/modules/issues/8750) - new module: bascule
- [#8835](https://github.com/nf-core/modules/issues/8835) - new module: slaf
- [#8877](https://github.com/nf-core/modules/issues/8877) - new module: hictk/load

## 5. Very Stale - No update >1 year, no stale label (93 issues)

Recommend closing or adding stale label.

### Bugs (16)

| Issue | Age (updated) | Title |
|-------|---------------|-------|
| [#2188](https://github.com/nf-core/modules/issues/2188) | 1234d | Pipelines do not work on ARM systems (e.g. Macbooks with M1/M2) |
| [#3654](https://github.com/nf-core/modules/issues/3654) | 953d | Multiple samtools modules use task.cpus-1 without checking for lower boundary |
| [#5395](https://github.com/nf-core/modules/issues/5395) | 703d | PIGZ_UNCOMPRESS causes groovyjarjarantlr4.v4.runtime.LexerNoViableAltException |
| [#5402](https://github.com/nf-core/modules/issues/5402) | 702d | Picard sortsam does not include the $args input in the command line |
| [#5522](https://github.com/nf-core/modules/issues/5522) | 674d | Addition of `samtools cat` in the samtools_sort module broke compatibility with  |
| [#5545](https://github.com/nf-core/modules/issues/5545) | 668d | modules/nf-core/gawk conda env is broken on some linux distrib |
| [#5547](https://github.com/nf-core/modules/issues/5547) | 659d | nf-test Github actions decompress automatically tar.gz outputs when they should  |
| [#5693](https://github.com/nf-core/modules/issues/5693) | 643d | Ultraplex output channel fastq includes no_match.fastq.gz |
| [#5967](https://github.com/nf-core/modules/issues/5967) | 587d | IGVREPORTS: wrong variable name |
| [#6189](https://github.com/nf-core/modules/issues/6189) | 561d | fastq outputs are missed during cellranger mkfastq due to directory structure |
| [#6197](https://github.com/nf-core/modules/issues/6197) | 560d | FASTQ_TRIM_FASTP_FASTQC:FASTP declares 5 input channels but 4 were specified |
| [#6607](https://github.com/nf-core/modules/issues/6607) | 539d | nf-test failure: subworkflow `BAM_VARIANT_DEMIX_BOOT_FREYJA` |
| [#6640](https://github.com/nf-core/modules/issues/6640) | 532d | Tests don't run for template updates |
| [#6696](https://github.com/nf-core/modules/issues/6696) | 515d | versions.yml-generating code produce malformed files without the nf-module faili |
| [#6637](https://github.com/nf-core/modules/issues/6637) | 488d | RTGtools missing in modules happy/happy |
| [#7292](https://github.com/nf-core/modules/issues/7292) | 413d | Investigate star failures on CI with docker_self_hosted |

### New Module Requests (17)

| Issue | Age (updated) | Title |
|-------|---------------|-------|
| [#4349](https://github.com/nf-core/modules/issues/4349) | 833d | new module: add modules from nf-core/readsimulator to nf-core/modules |
| [#4443](https://github.com/nf-core/modules/issues/4443) | 822d | new module: FACETS |
| [#4502](https://github.com/nf-core/modules/issues/4502) | 821d | new module: gridss/assembly |
| [#4499](https://github.com/nf-core/modules/issues/4499) | 821d | new module: gridss/preprocess |
| [#4375](https://github.com/nf-core/modules/issues/4375) | 711d | new module: ArchR |
| [#4440](https://github.com/nf-core/modules/issues/4440) | 700d | new module: RESEQ/RESEQ |
| [#5903](https://github.com/nf-core/modules/issues/5903) | 605d | new module: makeCGI |
| [#5924](https://github.com/nf-core/modules/issues/5924) | 602d | new module: usearch/unoise3 |
| [#5865](https://github.com/nf-core/modules/issues/5865) | 599d | new module: DRSTest/DRSTest01 |
| [#6080](https://github.com/nf-core/modules/issues/6080) | 575d | new module: TAPESTRY |
| [#6142](https://github.com/nf-core/modules/issues/6142) | 568d | new module: imc2mc |
| [#6163](https://github.com/nf-core/modules/issues/6163) | 564d | new module: picard/collecttargetedpcrmetrics |
| [#6162](https://github.com/nf-core/modules/issues/6162) | 564d | new module: taxonkit/reformat |
| [#6192](https://github.com/nf-core/modules/issues/6192) | 561d | new module: METABINNER/GENCOVERAGEFILE |
| [#6351](https://github.com/nf-core/modules/issues/6351) | 550d | new module: AGeNT |
| [#6420](https://github.com/nf-core/modules/issues/6420) | 548d | new module: grenedalf |
| [#6494](https://github.com/nf-core/modules/issues/6494) | 546d | new module: pretext/pretextgraph |

### Enhancements (3)

| Issue | Age (updated) | Title |
|-------|---------------|-------|
| [#1783](https://github.com/nf-core/modules/issues/1783) | 1326d | [FEATURE] Add a new label for internet-connected modules |
| [#2330](https://github.com/nf-core/modules/issues/2330) | 1219d | emitting metrics (info,stat,summaries) from modules for analytics and db ingesti |
| [#3822](https://github.com/nf-core/modules/issues/3822) | 829d | Add a parameter corresponding to -canonList <file> option of snpEff ann |

### Other (53)

| Issue | Age (updated) | Title |
|-------|---------------|-------|
| [#2604](https://github.com/nf-core/modules/issues/2604) | 1183d | Support running gatk4/cnnscorevariants over Conda |
| [#2628](https://github.com/nf-core/modules/issues/2628) | 1178d | [FEATURE] Modules for Batch tasks |
| [#2978](https://github.com/nf-core/modules/issues/2978) | 1067d | Update index handling in bam subworkflows |
| [#3778](https://github.com/nf-core/modules/issues/3778) | 919d | Update pointers to test data to static GitHub links |
| [#3789](https://github.com/nf-core/modules/issues/3789) | 912d | Number of cpu is not adapted for fastp tool |
| [#3960](https://github.com/nf-core/modules/issues/3960) | 870d | [FEATURE] Be smarter about the test we want to skip |
| [#4016](https://github.com/nf-core/modules/issues/4016) | 865d | Improve the way of reading input matrix files in R templates |
| [#4044](https://github.com/nf-core/modules/issues/4044) | 863d | [FEATURE]  Use Groovy to unpack compressed tar.gz files |
| [#4206](https://github.com/nf-core/modules/issues/4206) | 857d | Create a workflow to test module multiqc compatibility |
| [#4171](https://github.com/nf-core/modules/issues/4171) | 844d | Manage Module maintainers |
| [#4305](https://github.com/nf-core/modules/issues/4305) | 842d | Pipe zipped files in blast suite |
| [#4495](https://github.com/nf-core/modules/issues/4495) | 821d | [FEATURE] Add nf-test to subworkflow bcl_demultiplex |
| [#4687](https://github.com/nf-core/modules/issues/4687) | 781d | [FEATURE] Clearer documentation in on writing `nf-test` tests with multiple inpu |
| [#3894](https://github.com/nf-core/modules/issues/3894) | 781d | FGBIO: GroupByUMI module fix |
| [#5295](https://github.com/nf-core/modules/issues/5295) | 708d | add test to nf amps module |
| [#5350](https://github.com/nf-core/modules/issues/5350) | 707d | [FEATURE] about nf-core modules that runs a template script |
| [#4311](https://github.com/nf-core/modules/issues/4311) | 667d | Best practices for multiple process inputs |
| [#5602](https://github.com/nf-core/modules/issues/5602) | 653d | Add `deprecated` flag for deprecated modules |
| [#5690](https://github.com/nf-core/modules/issues/5690) | 644d | [FEATURE] adapt mygene to also extract pathway annotations |
| [#5704](https://github.com/nf-core/modules/issues/5704) | 641d | Investigate non consistent versions for cat_fastq module |
| [#5723](https://github.com/nf-core/modules/issues/5723) | 638d | update container for propr module |
| [#5750](https://github.com/nf-core/modules/issues/5750) | 632d | [FEATURE] Allow for the output of fastq files from fastqscreen_fastqscreen |
| [#4217](https://github.com/nf-core/modules/issues/4217) | 624d | Renovate nice-to-haves |
| [#5833](https://github.com/nf-core/modules/issues/5833) | 618d | Support multiple different CPU architectures |
| [#5831](https://github.com/nf-core/modules/issues/5831) | 617d | Add EDAM ontologies for input and output channels in `meta.yml` |
| [#5909](https://github.com/nf-core/modules/issues/5909) | 604d | Use "Dagger for GitHub" to clean up CI and make it more portable  |
| [#6029](https://github.com/nf-core/modules/issues/6029) | 583d | Standardized channel output for different files |
| [#5970](https://github.com/nf-core/modules/issues/5970) | 575d | Investigate issue extracting minigut_cf.tar.gz for centrifuge |
| [#6096](https://github.com/nf-core/modules/issues/6096) | 571d | new subworkflow gatk4/recalibrate (bam_baserecalibrator) |
| [#5848](https://github.com/nf-core/modules/issues/5848) | 561d | Swap test file paths to use `testdata_base_path` |
| [#6454](https://github.com/nf-core/modules/issues/6454) | 547d | [FEATURE] Update modules to include arity in path. |
| [#6650](https://github.com/nf-core/modules/issues/6650) | 529d | Update output to use type dir  |
| [#6689](https://github.com/nf-core/modules/issues/6689) | 520d | [FEATURE] bbmap/align control output better |
| [#6744](https://github.com/nf-core/modules/issues/6744) | 508d | Run singularity test only in merge-queue |
| [#6791](https://github.com/nf-core/modules/issues/6791) | 499d | Improvement/Bugfix: Update usage of lfcShrink for testing for diff. expression w |
| [#5834](https://github.com/nf-core/modules/issues/5834) | 499d | Use `eval` to collect version |
| [#6829](https://github.com/nf-core/modules/issues/6829) | 490d | update nf-core module: PROPR/PROPD |
| [#6821](https://github.com/nf-core/modules/issues/6821) | 487d | update module: bowtie2 |
| [#6830](https://github.com/nf-core/modules/issues/6830) | 485d | update nf-core module: PROPR/PROPR |
| [#6890](https://github.com/nf-core/modules/issues/6890) | 476d | [FEATURE] FASTQSCREEN_FASTQSCREEN should accept multiple inputs with a single da |
| [#7018](https://github.com/nf-core/modules/issues/7018) | 465d | Address limitations of using nf-test sharding |
| [#7017](https://github.com/nf-core/modules/issues/7017) | 465d | Create conda-fail.yml on Conda CI failures |
| [#7045](https://github.com/nf-core/modules/issues/7045) | 462d | Remove `params.hisat2_build_memory` from `hisat2/build` |
| [#7128](https://github.com/nf-core/modules/issues/7128) | 454d | CI: nf-test shard jobs to have test/tag names |
| [#6835](https://github.com/nf-core/modules/issues/6835) | 452d | update nf-core module: MYGENE |
| [#6505](https://github.com/nf-core/modules/issues/6505) | 448d | Snapshot content of version files instead of a hash |
| [#6694](https://github.com/nf-core/modules/issues/6694) | 442d | [FEATURE] Build automation for fetching Seqera Containers |
| [#6504](https://github.com/nf-core/modules/issues/6504) | 442d | Add renovate comments to environment.yml |
| [#5835](https://github.com/nf-core/modules/issues/5835) | 442d | Use Conda lock files |
| [#6831](https://github.com/nf-core/modules/issues/6831) | 424d | update nf-core module: PROPR/GREA |
| [#7321](https://github.com/nf-core/modules/issues/7321) | 407d | Limit STAR Memory |
| [#7390](https://github.com/nf-core/modules/issues/7390) | 389d | new module: hifiadapterfilt |
| [#7290](https://github.com/nf-core/modules/issues/7290) | 388d | Add module edgeR |

## 6. Stale - No update 6-12 months (61 issues)

| Issue | Age (updated) | Labels | Title |
|-------|---------------|--------|-------|
| [#6629](https://github.com/nf-core/modules/issues/6629) | 359d | (none) | Improve module specific resource requests |
| [#7766](https://github.com/nf-core/modules/issues/7766) | 354d | good first issue, nf-test | Test names in freebayes test do not fit the used test data |
| [#6737](https://github.com/nf-core/modules/issues/6737) | 353d | good first issue, update subworkflow, subworkflows | Update the `meta.yml` of subworkflows |
| [#1754](https://github.com/nf-core/modules/issues/1754) | 353d | bug, enhancement | [FEATURE] Fix bioconda recipe for deepvariant |
| [#6430](https://github.com/nf-core/modules/issues/6430) | 352d | question, new subworkflow, sarek | new subworkflow bam_to_cram |
| [#5516](https://github.com/nf-core/modules/issues/5516) | 352d | bug | Unexpected behaviour of cat/cat |
| [#5473](https://github.com/nf-core/modules/issues/5473) | 352d | bug, good first issue | Update test checksums in seqkit modules to allow for upgrades |
| [#5147](https://github.com/nf-core/modules/issues/5147) | 352d | (none) | [FEATURE] New Github Actions workflow based on nf-test files |
| [#4503](https://github.com/nf-core/modules/issues/4503) | 352d | new module | new module: gridss/variantcall |
| [#4261](https://github.com/nf-core/modules/issues/4261) | 352d | good first issue | Add `.bai` as an optional output of samtools/merge |
| [#1396](https://github.com/nf-core/modules/issues/1396) | 352d | (none) | Come up with a standard & documentation on subworkflows |
| [#243](https://github.com/nf-core/modules/issues/243) | 352d | enhancement, tests, hackathon2023 | Implement unit-test for full datasets |
| [#6007](https://github.com/nf-core/modules/issues/6007) | 351d | new module | new module: MSISENSORPRO/MSISENSORPRO_TUMOR_ONLY |
| [#5143](https://github.com/nf-core/modules/issues/5143) | 351d | (none) | Create bioconda container for propr |
| [#5008](https://github.com/nf-core/modules/issues/5008) | 351d | bug | BCLconvert broken on ARM since v4.2.4 |
| [#4744](https://github.com/nf-core/modules/issues/4744) | 351d | (none) | [FEATURE] Use a topic specific example in the description for `meta` |
| [#4722](https://github.com/nf-core/modules/issues/4722) | 351d | (none) | Check out if we really can remove these old tests in custom/sratoolsnc |
| [#3799](https://github.com/nf-core/modules/issues/3799) | 351d | bug | Update a few container declarations  |
| [#3455](https://github.com/nf-core/modules/issues/3455) | 351d | (none) | [FEATURE] Disabling JVM Hotspot in modules for JAVA tools |
| [#3254](https://github.com/nf-core/modules/issues/3254) | 351d | (none) | [FEATURE] make picard markduplicates smarter |
| [#3069](https://github.com/nf-core/modules/issues/3069) | 351d | bug | Create biscuit tabix bgzip image |
| [#2547](https://github.com/nf-core/modules/issues/2547) | 351d | bug | MD5SUM hits docker pull limit |
| [#2322](https://github.com/nf-core/modules/issues/2322) | 351d | bug | deeptools_bamcoverage fails silently |
| [#1984](https://github.com/nf-core/modules/issues/1984) | 351d | enhancement | [FEATURE] Support bigwigs in pints_caller module |
| [#1766](https://github.com/nf-core/modules/issues/1766) | 351d | (none) | [FEATURE] 'enhancement to existing module' template. |
| [#1688](https://github.com/nf-core/modules/issues/1688) | 351d | (none) | [FEATURE] STAR handle gzipped files |
| [#1450](https://github.com/nf-core/modules/issues/1450) | 351d | (none) | Input naming conventions |
| [#258](https://github.com/nf-core/modules/issues/258) | 351d | hackathon2023 | [FEATURE]: Ask for slightly less memory for tools with explicit task.m |
| [#7799](https://github.com/nf-core/modules/issues/7799) | 350d | new module | new module: TOOL/SUBTOOL plink-PCA |
| [#7368](https://github.com/nf-core/modules/issues/7368) | 350d | (none) | [FEATURE] use `arity` in freebayes module to allow more than two input |
| [#7165](https://github.com/nf-core/modules/issues/7165) | 350d | new module | new module: PALOM |
| [#5972](https://github.com/nf-core/modules/issues/5972) | 350d | help wanted | Investigate unknown issue for checkv/updatedatabase module |
| [#5795](https://github.com/nf-core/modules/issues/5795) | 350d | (none) | Use Renovate for Nextflow versions |
| [#5710](https://github.com/nf-core/modules/issues/5710) | 350d | new module | new module: tanoti |
| [#5210](https://github.com/nf-core/modules/issues/5210) | 350d | (none) | [MODULE] velocyto.py module for nf-core/scrnaseq |
| [#4176](https://github.com/nf-core/modules/issues/4176) | 350d | new module | new module: picard/samtofastq |
| [#3918](https://github.com/nf-core/modules/issues/3918) | 350d | (none) | [FEATURE] subworkflows/multiple_impute_glimpse2 |
| [#3913](https://github.com/nf-core/modules/issues/3913) | 350d | (none) | Add alternate shrinkage methodology to deseq2/differential |
| [#3864](https://github.com/nf-core/modules/issues/3864) | 350d | (none) | Add igenomes dedicated utils  |
| [#7247](https://github.com/nf-core/modules/issues/7247) | 347d | new module | new module: leafcutter/clusterregtools |
| [#7246](https://github.com/nf-core/modules/issues/7246) | 347d | new module | new module: leafcutter/differential_splicing |
| [#7157](https://github.com/nf-core/modules/issues/7157) | 347d | new module | new module: CAREamics |
| [#4350](https://github.com/nf-core/modules/issues/4350) | 347d | bug | ART/ILLUMINA module currently doesn't allow -c option |
| [#4598](https://github.com/nf-core/modules/issues/4598) | 346d | new module | new module: hicqc |
| [#7848](https://github.com/nf-core/modules/issues/7848) | 345d | new module | new module: SegmentationBenchmark |
| [#7882](https://github.com/nf-core/modules/issues/7882) | 343d | new module | imzML Converter |
| [#7880](https://github.com/nf-core/modules/issues/7880) | 343d | enhancement | create module parse tx fasta |
| [#7889](https://github.com/nf-core/modules/issues/7889) | 342d | new module | new module: ampliconsorter |
| [#7888](https://github.com/nf-core/modules/issues/7888) | 342d | new module | new module: ontbarcoder |
| [#7887](https://github.com/nf-core/modules/issues/7887) | 342d | new module | new module: astral |
| [#7886](https://github.com/nf-core/modules/issues/7886) | 342d | new module | new module: cactus |
| [#5202](https://github.com/nf-core/modules/issues/5202) | 341d | bug | fastp failed reads does not write paired, failed reads  |
| [#7945](https://github.com/nf-core/modules/issues/7945) | 340d | new module | Cardinal Preprocessing |
| [#7943](https://github.com/nf-core/modules/issues/7943) | 340d | new module | new module: maaslin2 |
| [#7936](https://github.com/nf-core/modules/issues/7936) | 340d | update module | parameterize arguments for rtgtools_vcfeval |
| [#7901](https://github.com/nf-core/modules/issues/7901) | 340d | (none) | ensemblvep/vep |
| [#7884](https://github.com/nf-core/modules/issues/7884) | 340d | new module | Cardinal Data import |
| [#7883](https://github.com/nf-core/modules/issues/7883) | 340d | new module | msConvert module |
| [#7865](https://github.com/nf-core/modules/issues/7865) | 340d | enhancement, question | Dealing with asynchronous metadata |
| [#7864](https://github.com/nf-core/modules/issues/7864) | 340d | enhancement | Enable onError in BUSCO |
| [#7863](https://github.com/nf-core/modules/issues/7863) | 340d | enhancement | Update the nextflow config for BUSCO with error stratergy |
| [#7858](https://github.com/nf-core/modules/issues/7858) | 340d | new module | Migrate MANIFEST_STATS to nextflow_modules |
| [#7857](https://github.com/nf-core/modules/issues/7857) | 340d | new module | Migrate MANIFEST module to nextflow_modules |
| [#7856](https://github.com/nf-core/modules/issues/7856) | 340d | new module | Migrate the AMEND_GENOME_DATA module to nextflow_module |
| [#7851](https://github.com/nf-core/modules/issues/7851) | 340d | new module | Create nf-test for prepare_metadata subworkflow |
| [#7850](https://github.com/nf-core/modules/issues/7850) | 340d | new module | new module: metadata/fetch.nf |
| [#7849](https://github.com/nf-core/modules/issues/7849) | 340d | new subworkflow | new subworkflow: Prepare metadata as a subworkflow |
| [#3821](https://github.com/nf-core/modules/issues/3821) | 340d | enhancement | Add --annotate flag to CNVKIT_BATCH |
| [#8062](https://github.com/nf-core/modules/issues/8062) | 339d | update module | update module: update GATK Mutect2 to identifies mutations in the indi |
| [#8034](https://github.com/nf-core/modules/issues/8034) | 339d | bug | `BIOHANSEL` inconsistency unitest between conda and containers |
| [#8001](https://github.com/nf-core/modules/issues/8001) | 339d | (none) | Identify optional inputs (files) |
| [#8000](https://github.com/nf-core/modules/issues/8000) | 339d | (none) | Identify required inputs |
| [#7999](https://github.com/nf-core/modules/issues/7999) | 339d | tests, nf-test | Identify test data for nf-test for this module |
| [#7998](https://github.com/nf-core/modules/issues/7998) | 339d | documentation, update module | update module: RTGTOOLS/ROCPLOT |
| [#7996](https://github.com/nf-core/modules/issues/7996) | 339d | documentation, update module | update module: RTGTOOLS/PEDFILTER |
| [#7995](https://github.com/nf-core/modules/issues/7995) | 339d | documentation, update module | update module: RTGTOOLS/VCFEVAL |
| [#7989](https://github.com/nf-core/modules/issues/7989) | 339d | update module | update module: mainmap2/align into main |
| [#7988](https://github.com/nf-core/modules/issues/7988) | 339d | update module | update module: chopper  integrate into main.nf  |
| [#7962](https://github.com/nf-core/modules/issues/7962) | 339d | new module | new module: earlgrey/earlgrey |
| [#7938](https://github.com/nf-core/modules/issues/7938) | 339d | (none) | DSL1 > DSL2 migration |
| [#7937](https://github.com/nf-core/modules/issues/7937) | 339d | (none) | Approved pipelines fail using test data using `test,docker` |
| [#7894](https://github.com/nf-core/modules/issues/7894) | 339d | new module | new module: rtgtools/vcffilter |
| [#7878](https://github.com/nf-core/modules/issues/7878) | 339d | new module | METASPACE API submission |
| [#7877](https://github.com/nf-core/modules/issues/7877) | 339d | new module | METASPACE to S2IsoMEr |
| [#7860](https://github.com/nf-core/modules/issues/7860) | 339d | new module | Migrate PROCESS_SEQ_REGION to nextflow_modules |
| [#7853](https://github.com/nf-core/modules/issues/7853) | 339d | new module | new module: metabuli/classify |
| [#8108](https://github.com/nf-core/modules/issues/8108) | 338d | update module | update module: rsem/calculateexpression and rsem/preparereference |
| [#8002](https://github.com/nf-core/modules/issues/8002) | 338d | (none) | Template for Javascript filters |
| [#7942](https://github.com/nf-core/modules/issues/7942) | 338d | CI-issue | Update the CI/CD for genome_load_prepare |
| [#7792](https://github.com/nf-core/modules/issues/7792) | 338d | bug | Inputs copied to work directory from scratch directory in GATK4SPARK_A |
| [#7496](https://github.com/nf-core/modules/issues/7496) | 338d | good first issue, new module | new module (collection): CRABS |
| [#7992](https://github.com/nf-core/modules/issues/7992) | 337d | (none) | add modules + subworkflow for protein activity |
| [#7956](https://github.com/nf-core/modules/issues/7956) | 337d | new module | Migrate compare_genome_stats to nextflow_modules |
| [#7842](https://github.com/nf-core/modules/issues/7842) | 337d | update module | Add nf-test to utils modules in nextflow_modules |
| [#7819](https://github.com/nf-core/modules/issues/7819) | 337d | new subworkflow | Create utils fuctions into modules in nextflow_modules |
| [#5962](https://github.com/nf-core/modules/issues/5962) | 336d | (none) | [FEATURE] Deprecate untarfiles |
| [#5916](https://github.com/nf-core/modules/issues/5916) | 336d | new module | new module: SHORAH/shorah |
| [#8164](https://github.com/nf-core/modules/issues/8164) | 333d | bug | GFASTATS fails when genome size positional argument is given |
| [#6845](https://github.com/nf-core/modules/issues/6845) | 331d | new module | new module: Segger |
| [#8239](https://github.com/nf-core/modules/issues/8239) | 325d | (none) | [BATCH] Module updates that do not require pipeline updates |
| [#8238](https://github.com/nf-core/modules/issues/8238) | 325d | (none) | [BATCH] Module updates requiring pipeline updates |
| [#8236](https://github.com/nf-core/modules/issues/8236) | 325d | nf-test | [FEATURE] nf-test assertions - use md5 sums for readLines |
| [#8252](https://github.com/nf-core/modules/issues/8252) | 324d | bug | Remove custom docker.runOptions from nextflow.configs living in tests  |
| [#3859](https://github.com/nf-core/modules/issues/3859) | 324d | enhancement | [FEATURE] output index files for GATK4_APPLYBQSR* modules |
| [#8347](https://github.com/nf-core/modules/issues/8347) | 311d | (none) | Are we adding successful builds to `meta.yml`? That'd be nice. Then we |
| [#8113](https://github.com/nf-core/modules/issues/8113) | 304d | bug | nf-core lint fails with eigenv variable name |
| [#7961](https://github.com/nf-core/modules/issues/7961) | 304d | bug | The `fastp` module will zero source FASTQ files if they end in `.fastp |
| [#7950](https://github.com/nf-core/modules/issues/7950) | 304d | bug | Fix bactmap module (ERROR ~ Cannot get property 'args' on null object) |
| [#7879](https://github.com/nf-core/modules/issues/7879) | 304d | new module | create module |
| [#7781](https://github.com/nf-core/modules/issues/7781) | 304d | bug | Linting fails for module with Dockerfile |
| [#7226](https://github.com/nf-core/modules/issues/7226) | 304d | (none) | Parabricks modules need `stageInMode 'copy'` |
| [#6708](https://github.com/nf-core/modules/issues/6708) | 304d | bug | nf-core install could not detect work dir |
| [#8383](https://github.com/nf-core/modules/issues/8383) | 303d | (none) | [FEATURE] Generate README automatically to reflect current nf-core/too |
| [#8393](https://github.com/nf-core/modules/issues/8393) | 298d | (none) | [FEATURE] Output genomicsdb interval_list for downstream processing |
| [#8582](https://github.com/nf-core/modules/issues/8582) | 270d | bug | rseqc/junctionannotation fails linting |
| [#5200](https://github.com/nf-core/modules/issues/5200) | 262d | new module | new module: zellkonverter/AnnData-Conversion |
| [#6866](https://github.com/nf-core/modules/issues/6866) | 261d | new module | New module: dorado |
| [#8686](https://github.com/nf-core/modules/issues/8686) | 248d | update module | update module: stringtie/merge |
| [#7451](https://github.com/nf-core/modules/issues/7451) | 248d | bug | issues with gprofiler2/gost |
| [#8716](https://github.com/nf-core/modules/issues/8716) | 247d | (none) | [FEATURE] Update modules to remove undocumented task.ext fields |
| [#8740](https://github.com/nf-core/modules/issues/8740) | 241d | update module | update module: assess adding gawk to coreutils, and re-asses the gawk  |
| [#8757](https://github.com/nf-core/modules/issues/8757) | 237d | bug | Container for FASTQSCREEN_FASTQSCREEN should include bismark |
| [#8764](https://github.com/nf-core/modules/issues/8764) | 233d | (none) | [FEATURE] Let HIPHASE return the phased bam file |
| [#8594](https://github.com/nf-core/modules/issues/8594) | 230d | (none) | Turn off dockerfile arm builds |
| [#8786](https://github.com/nf-core/modules/issues/8786) | 224d | bug | gprofiler generated GMT does not match the fitlering that the gprofile |
| [#8676](https://github.com/nf-core/modules/issues/8676) | 221d | bug | Attempting to install seqkit modules results in no change |
| [#8535](https://github.com/nf-core/modules/issues/8535) | 221d | new subworkflow, wishlist | new subworkflow: FASTA_BGZIP_INDEX_DICT_SAMTOOLS |
| [#8820](https://github.com/nf-core/modules/issues/8820) | 213d | (none) | update cnvkit/batch output channels |
| [#8587](https://github.com/nf-core/modules/issues/8587) | 213d | bug | XeniumRanger import-segmentation failed on Tower |
| [#4519](https://github.com/nf-core/modules/issues/4519) | 213d | (none) | Use of OCI Containers |
| [#8424](https://github.com/nf-core/modules/issues/8424) | 208d | new module, wishlist | new module: manta/annotate |
| [#8423](https://github.com/nf-core/modules/issues/8423) | 208d | new module, wishlist | new module: svaba/annotate |
| [#8422](https://github.com/nf-core/modules/issues/8422) | 208d | new module, wishlist | new module: gridss/annotate |
| [#8700](https://github.com/nf-core/modules/issues/8700) | 205d | (none) | [FEATURE] gProfiler separate enrichment for up and down-regulated gene |
| [#4570](https://github.com/nf-core/modules/issues/4570) | 204d | enhancement | [FEATURE] Add `stub` support to every module |
| [#7439](https://github.com/nf-core/modules/issues/7439) | 201d | new module | new module: rattle/cluster |
| [#8884](https://github.com/nf-core/modules/issues/8884) | 200d | (none) | [FEATURE] Add GPU support to deepvariant/rundeepvariant |
| [#8007](https://github.com/nf-core/modules/issues/8007) | 200d | update module, nf-test | update module: need to create tests for getorganelle/fromreads |
| [#5409](https://github.com/nf-core/modules/issues/5409) | 199d | bug, good first issue | Module stub that `touch .gz` break snapshots in `nf-test` |
| [#8899](https://github.com/nf-core/modules/issues/8899) | 197d | (none) | cnvkit/batch stub tests need improvements |
| [#8847](https://github.com/nf-core/modules/issues/8847) | 196d | (none) | [FEATURE] use nodefaults for all conda environments |
| [#5546](https://github.com/nf-core/modules/issues/5546) | 193d | new module | new module: spacemarkers |
| [#8927](https://github.com/nf-core/modules/issues/8927) | 191d | (none) | Fix sentieon dedup metrics now that multiqc can handle it |
| [#8460](https://github.com/nf-core/modules/issues/8460) | 187d | new module, wishlist | new module: fastlmm |
| [#7918](https://github.com/nf-core/modules/issues/7918) | 181d | bug, good first issue | update stub: pharokka/installdatabases |

## 7. Topic Channel Migration (101 issues)

Umbrella: [#9978](https://github.com/nf-core/modules/issues/9978). All pending, none completed. Tagged `good first issue`. Leave open.

## 8. Active/Recent Issues (102 issues)

Updated within last 6 months. Leave open.

| Issue | Updated | Labels | Title |
|-------|---------|--------|-------|
| [#10282](https://github.com/nf-core/modules/issues/10282) | 0d ago | new module | new module: SAMTOOLS/ADDREPLACERG |
| [#4211](https://github.com/nf-core/modules/issues/4211) | 0d ago | (none) | Renovate Dashboard 🤖 |
| [#10269](https://github.com/nf-core/modules/issues/10269) | 1d ago | new module | new module: KMERGENIE |
| [#10267](https://github.com/nf-core/modules/issues/10267) | 1d ago | update module | update module: crabz/decompress |
| [#10249](https://github.com/nf-core/modules/issues/10249) | 2d ago | update module | update module: subread/featurecounts |
| [#10248](https://github.com/nf-core/modules/issues/10248) | 3d ago | (none) | [FEATURE] remove params from  modules and subworkflows |
| [#8583](https://github.com/nf-core/modules/issues/8583) | 3d ago | bug | narfmap/hashtable tests fail because of an out of memory error |
| [#10127](https://github.com/nf-core/modules/issues/10127) | 4d ago | (none) | new module: updhmm |
| [#9978](https://github.com/nf-core/modules/issues/9978) | 4d ago | good first issue | Adopt topic channels in all nf-core modules |
| [#9984](https://github.com/nf-core/modules/issues/9984) | 5d ago | new module, wishlist | new module: seqkit/sample |
| [#9653](https://github.com/nf-core/modules/issues/9653) | 5d ago | new module, wishlist | new module: ViralConsensus |
| [#9461](https://github.com/nf-core/modules/issues/9461) | 5d ago | new module, wishlist | new module: graphtyper/genotypesv |
| [#9355](https://github.com/nf-core/modules/issues/9355) | 5d ago | new module, wishlist | new module: kMetaShot |
| [#10073](https://github.com/nf-core/modules/issues/10073) | 10d ago | new module | new module: macsyfinder |
| [#10054](https://github.com/nf-core/modules/issues/10054) | 11d ago | new module | new module: gatk4/analyzecovariates |
| [#10026](https://github.com/nf-core/modules/issues/10026) | 14d ago | new module | new module: guacamole |
| [#9996](https://github.com/nf-core/modules/issues/9996) | 15d ago | new module | new module: VARIANT-EXTRACTOR |
| [#10005](https://github.com/nf-core/modules/issues/10005) | 15d ago | bug | Wrong argument type in log.debug |
| [#9942](https://github.com/nf-core/modules/issues/9942) | 18d ago | new module | new module: telescope/assign |
| [#9224](https://github.com/nf-core/modules/issues/9224) | 19d ago | new module, wishlist | new module: BCFTOOLS/PLUGINVCF2TABLE |
| [#9891](https://github.com/nf-core/modules/issues/9891) | 22d ago | bug | bam_tumor_only_somatic_variant_calling_gatk: Input channel structure m |
| [#9487](https://github.com/nf-core/modules/issues/9487) | 28d ago | enhancement, WIP, update module, rnaseq | update module: HISAT2/ALIGN |
| [#9798](https://github.com/nf-core/modules/issues/9798) | 29d ago | bug | [Bug] meta_fb never defined in CELLRANGER_MULTI |
| [#9792](https://github.com/nf-core/modules/issues/9792) | 30d ago | update module | Bump  BCFTOOLS version to 1.23 |
| [#9269](https://github.com/nf-core/modules/issues/9269) | 30d ago | (none) | Migrate nf-core/variantprioritization modules to topic channels |
| [#9149](https://github.com/nf-core/modules/issues/9149) | 30d ago | bug | cellpose 3.1.0 interprets 3D TIFFs as Z-stacks rather than channels by |
| [#8699](https://github.com/nf-core/modules/issues/8699) | 31d ago | new module, wishlist | new module: RMATS |
| [#9706](https://github.com/nf-core/modules/issues/9706) | 38d ago | new module | new module: intervene/upset |
| [#8032](https://github.com/nf-core/modules/issues/8032) | 42d ago | bug, conda-fail | nf-test failing for pharokka |
| [#9647](https://github.com/nf-core/modules/issues/9647) | 44d ago | bug | Multiple uses of seqkit replace module fail due to output/input name c |
| [#9646](https://github.com/nf-core/modules/issues/9646) | 44d ago | bug | seqkit replace incorrectly uses the '-i' flag |
| [#2159](https://github.com/nf-core/modules/issues/2159) | 47d ago | new subworkflow, update subworkflow, sarek, subworkflows | Port sarek subworkflows to nf-core/modules |
| [#9623](https://github.com/nf-core/modules/issues/9623) | 51d ago | bug | gatk4/markduplicates and picard/markduplicates output file extension c |
| [#9619](https://github.com/nf-core/modules/issues/9619) | 51d ago | new module | new module: gapseq |
| [#9231](https://github.com/nf-core/modules/issues/9231) | 72d ago | new module | new module: DEVIDER |
| [#9423](https://github.com/nf-core/modules/issues/9423) | 73d ago | update module | update module: FLYE |
| [#9573](https://github.com/nf-core/modules/issues/9573) | 73d ago | bug | utils_nfcore_pipeline: Positional args warning is misleading |
| [#9561](https://github.com/nf-core/modules/issues/9561) | 77d ago | bug | FASTQC command number expected for "--memory" |
| [#9449](https://github.com/nf-core/modules/issues/9449) | 80d ago | new module, wishlist | new module: peakScout/peak2gene |
| [#9382](https://github.com/nf-core/modules/issues/9382) | 80d ago | update module | update module:  METAPHLAN/METAPHLAN_METAPHALAN add flag to run with `- |
| [#9527](https://github.com/nf-core/modules/issues/9527) | 81d ago | update module | BWA_INDEX just needs an update like BWAMEM2_INDEX in PR#8993 |
| [#9001](https://github.com/nf-core/modules/issues/9001) | 81d ago | new module, wishlist | new module: dnaapler |
| [#6698](https://github.com/nf-core/modules/issues/6698) | 87d ago | (none) | Bulk update modules to use Seqera Containers |
| [#5832](https://github.com/nf-core/modules/issues/5832) | 87d ago | container-issue | [META-ISSUE] Migrate modules to Seqera Containers |
| [#8109](https://github.com/nf-core/modules/issues/8109) | 89d ago | new module | new module: deconwolf |
| [#9424](https://github.com/nf-core/modules/issues/9424) | 95d ago | bug | Sendmail issue when running on AWS batch with S3 as workDir |
| [#9421](https://github.com/nf-core/modules/issues/9421) | 101d ago | update module | update module: BACKSUB |
| [#9418](https://github.com/nf-core/modules/issues/9418) | 101d ago | (none) | [FEATURE] cellranger multi: leverage new reference-free VDJ option |
| [#7016](https://github.com/nf-core/modules/issues/7016) | 101d ago | (none) | Handle GitHub runners possibly running out of space |
| [#8169](https://github.com/nf-core/modules/issues/8169) | 103d ago | new module | new module: varify |
| [#9230](https://github.com/nf-core/modules/issues/9230) | 105d ago | bug | parabricks/fq2bam needs the fasta in the same folder as the BWAIndex |
| [#9401](https://github.com/nf-core/modules/issues/9401) | 106d ago | bug | Bowtie2 + Samtools pipeline in nf-core module may use double the inten |
| [#9366](https://github.com/nf-core/modules/issues/9366) | 108d ago | new module | new module: Baltica |
| [#5599](https://github.com/nf-core/modules/issues/5599) | 111d ago | new module | new list of proteomics modules |
| [#9354](https://github.com/nf-core/modules/issues/9354) | 113d ago | enhancement, tests, nf-test | Properly test the cram output of bwa/mem and bwamem2/mem |
| [#9339](https://github.com/nf-core/modules/issues/9339) | 114d ago | new module | new module: rgi/bwt |
| [#9307](https://github.com/nf-core/modules/issues/9307) | 120d ago | bug | Wrong output definition in wisecondorx/predict |
| [#9298](https://github.com/nf-core/modules/issues/9298) | 121d ago | new module | new module:ena-webin-cli |
| [#9291](https://github.com/nf-core/modules/issues/9291) | 121d ago | (none) | Track GitHub Actions CO2 usage |
| [#9268](https://github.com/nf-core/modules/issues/9268) | 122d ago | update module | update module: vcf2zarr/convert |
| [#9263](https://github.com/nf-core/modules/issues/9263) | 122d ago | update module | update module: BISMARK_ALIGN - add version topic |
| [#9262](https://github.com/nf-core/modules/issues/9262) | 122d ago | update module | update module: TRINITY  - add version topic |
| [#9261](https://github.com/nf-core/modules/issues/9261) | 122d ago | new module | update module: FASTQC - add version topic |
| [#9260](https://github.com/nf-core/modules/issues/9260) | 122d ago | update module | update module: TRIMGALORE - add version topic |
| [#9259](https://github.com/nf-core/modules/issues/9259) | 122d ago | update module | update module: MULTIQC - add version topic |
| [#9258](https://github.com/nf-core/modules/issues/9258) | 122d ago | update module | update module: TABIX_TABIX - add version topic |
| [#9257](https://github.com/nf-core/modules/issues/9257) | 122d ago | bug | Peddy can no longer be run without providing sites argument |
| [#9222](https://github.com/nf-core/modules/issues/9222) | 129d ago | update module | update module: PROPR/PROPD |
| [#9221](https://github.com/nf-core/modules/issues/9221) | 129d ago | bug | Samtools merge module not respecting prefix |
| [#8270](https://github.com/nf-core/modules/issues/8270) | 129d ago | new module | new module: purecn/presegmented |
| [#9211](https://github.com/nf-core/modules/issues/9211) | 130d ago | new module | new module: onkopus |
| [#8331](https://github.com/nf-core/modules/issues/8331) | 130d ago | new module | new module: purecn/segmentedrun |
| [#8615](https://github.com/nf-core/modules/issues/8615) | 131d ago | new module, wishlist | new module: ANY2FASTA |
| [#8614](https://github.com/nf-core/modules/issues/8614) | 131d ago | new module, wishlist | new module: PARSNP |
| [#8563](https://github.com/nf-core/modules/issues/8563) | 131d ago | new module, wishlist | Expand gget/gget into different subtools like gget/blast, gget/ref ... |
| [#9208](https://github.com/nf-core/modules/issues/9208) | 133d ago | bug | getorganelle partial output |
| [#6782](https://github.com/nf-core/modules/issues/6782) | 133d ago | enhancement, new module, sarek | Integration of Parabricks |
| [#9200](https://github.com/nf-core/modules/issues/9200) | 134d ago | new module | new module: bin2cell |
| [#9199](https://github.com/nf-core/modules/issues/9199) | 134d ago | bug | deeparg hamronization meta.yml |
| [#9192](https://github.com/nf-core/modules/issues/9192) | 136d ago | bug | Using docker wave container throws  error message for some files |
| [#9191](https://github.com/nf-core/modules/issues/9191) | 136d ago | (none) | [FEATURE] Make `hostile/fetch` output compatible with `storeDir` by ex |
| [#9182](https://github.com/nf-core/modules/issues/9182) | 141d ago | new module | new module: modkit/dmr |
| [#9179](https://github.com/nf-core/modules/issues/9179) | 141d ago | bug | blast/blastdbcmd fails with big databases |
| [#5055](https://github.com/nf-core/modules/issues/5055) | 144d ago | new module, imaging | new module: BOMS |
| [#5126](https://github.com/nf-core/modules/issues/5126) | 145d ago | new module | new module: FICTURE |
| [#4906](https://github.com/nf-core/modules/issues/4906) | 145d ago | new subworkflow | new subworkflow: FASTQ/SHORTREADTRIMANDMERGE/ALLOFTHEM |
| [#9167](https://github.com/nf-core/modules/issues/9167) | 147d ago | new module | new module: stacks/ref_map |
| [#5148](https://github.com/nf-core/modules/issues/5148) | 153d ago | new module | new module: BAMixChecker |
| [#9092](https://github.com/nf-core/modules/issues/9092) | 162d ago | bug, tests, conda-fail, CI-issue | GATK4 conda failures |
| [#9081](https://github.com/nf-core/modules/issues/9081) | 163d ago | update module | update module: CLAIR3 |
| [#8805](https://github.com/nf-core/modules/issues/8805) | 163d ago | update module | update module: bwamem2/mem |
| [#9057](https://github.com/nf-core/modules/issues/9057) | 165d ago | new module | new module: ccsmeth |
| [#9041](https://github.com/nf-core/modules/issues/9041) | 165d ago | bug | AGAT_* 1.4.2 modules actually contain 1.4.1 |
| [#8888](https://github.com/nf-core/modules/issues/8888) | 167d ago | (none) | update stub: fcs/fcsadaptor |
| [#8887](https://github.com/nf-core/modules/issues/8887) | 167d ago | update module | update stub: gatk4/haplotypecaller |
| [#9011](https://github.com/nf-core/modules/issues/9011) | 172d ago | new module | new module: Spectre |
| [#4306](https://github.com/nf-core/modules/issues/4306) | 172d ago | (none) | Renovate Workflow  |
| [#9012](https://github.com/nf-core/modules/issues/9012) | 175d ago | new module | new module: SVIM |
| [#9010](https://github.com/nf-core/modules/issues/9010) | 175d ago | new module | new module: straglr |
| [#9009](https://github.com/nf-core/modules/issues/9009) | 175d ago | new module | new module: truvari/collapse |
| [#9003](https://github.com/nf-core/modules/issues/9003) | 175d ago | new module | new module: SciLifeLab DDS/createProject |
| [#8990](https://github.com/nf-core/modules/issues/8990) | 177d ago | new module | new module: FastReseg |

## Summary of Recommended Actions

| Action | Count |
|--------|-------|
| Close (already implemented) | 11 |
| Review partial implementations | 5 |
| Subcommand requests (keep open) | 4 |
| Batch-close stale-labeled | 21 |
| Add stale label / close (>1yr) | 89 |
| Ping / stale-label (6-12mo) | 145 |
| Leave open (topic migration) | 101 |
| Leave open (active) | 102 |