---
title: spring cleaning march 2023 modules
tags: spring cleaning, meeting notes, maintainers, modules
---

## Modules / subworkflows spring cleaning march 2023

### Tasks

1. Assign "stale" labels and comment the following message to all PRs and issues older than 1 year.
> Hi there!
>
> We've noticed there hasn't been much activity here. Are you still planning on working on this?
> If not, you can ignore this message and we'll close your PR/Issue in about 2 weeks
>
> Cheers
> the nf-core maintainers

**Important**: If PR/issue looks relevant, we can keep it for the hackathon (tag: `hackathon2023` or `good_first_issue`). If still present after the hackathon without further comments, we delete it.

2. Standardize meta.yml keywords: the left sidebar on `https://nf-co.re/modules` is very long and repetitive if tags are written with slight differences
3. Review and merge open PRs
4. Review open branches

### Task distribution

- Modules
- PRs (Matthias)
- tagged with `stale`, await responses :heavy_check_mark:
- PRs without responses: evaluate if they should be closed or go to hackathon board? Add `hackathon2023`tag in that case.
- review and merge open PRs
- issues (Jasmin, Louisa, Ram)
- tag all issues older than March 2022 with `stale` and send message :heavy_check_mark:
- check if stale issues have a PR associated and add #issue to PR if missing :heavy_check_mark:
- if still looks interesting, tag with `hackathon2023` instead :heavy_check_mark:
- Subworkflows (Ram, Nicolas)
- review PRs (as for modules)
- review issues (as for modules)
- check if subworkflows follow documentation standard, if not:
- fix small issues
- open issues for the hackathon (add `hackathon2023` tag)
- checklist (add your name after a subworkflow to divide the work):
- [x] bam_dedup_stats_samtools_umitools @nvnieuwk
- [x] bam_split_by_region @nvnieuwk
- [x] bed_scatter_bedtools @nvnieuwk
- [x] fastq_align_bwa @nvnieuwk
- [x] fastq_align_star @nvnieuwk
- [x] gatk_create_som_pon @nvnieuwk
- [x] vcf_annotate_snpeff @nvnieuwk
- [x] bam_markduplicates_picard @nvnieuwk
- [x] bam_stats_samtools @nvnieuwk
- [x] fasta_binning_concoct @nvnieuwk
- [x] fastq_align_bwaaln @nvnieuwk
- [x] fastq_contam_seqtk_kraken @nvnieuwk
- [x] gatk_tumor_normal_somatic_variant_calling @nvnieuwk
- [x] vcf_extract_relate_somalier @nvnieuwk
- [x] bam_qc_picard @ramprasadn
- [x] bam_variant_calling_freebayes @ramprasadn
- [x] fasta_index_dna @ramprasadn
- [x] fastq_align_chromap @ramprasadn
- [x] fastq_download_prefetch_fasterqdump_sratools @ramprasadn
- [ ] gatk_tumor_only_somatic_variant_calling @ramprasadn (get help!)
- [ ] vcf_gather_bcftools @ramprasadn
- [ ] bam_rseqc @ramprasadn
- [ ] bcl_demultiplex @ramprasadn
- [ ] fasta_newick_epang_gappa @ramprasadn
- [ ] fastq_align_dna
- [ ] fastq_fastqc_umitools_trimgalore
- [ ] homer
- [ ] vcf_impute_glimpse
- [ ] bam_sort_stats_samtools
- [ ] bedgraph_bedclip_bedgraphtobigwig
- [ ] fastq_align_bowtie2
- [ ] fastq_align_hisat2
- [ ] fastq_subsample_fq_salmon
- [ ] vcf_annotate_ensemblvep @matthdsm
> We don't have clear standards for input and output keys in the meta.yml for subworkflows. In some subworkflows we have defined the channels that come in, and in some the channel elements.https://nfcore.slack.com/archives/C043UU89KKQ/p1678441022781649?thread_ts=1678357250.085749&cid=C043UU89KKQ Need more clarity on this before we spend time making changes :D
- Metadata tags stadards (Jasmin, Louisa)
- **Website module filter** screens yaml files for:
- module title
- module description
- module keywords
- input channel names
- output channel names
- **Guidelines for choosing module keywords** (draft)
- check if your keyword already exists and avoid having redundancy
:arrow_forward: use `annotate` (_not_: `annotate, annotation, annotations`)
- do not include a module's title (it can already be found by that)
- if you want to mention certain tool names: mention those tools in the module description, not as keywords
:arrow_forward: e.g. AMPcombi summarizes output of multiple AMP tools like ampir, so you want AMPcombi to be found if someone searches for ampir
- use lowercase, do not join separate words
:arrow_forward: `taxonomic profiling` (_not_: `taxonomicprofiling`)
- uppercase only for abbreviations
:arrow_forward: `DNA`, `RNA`
- use space character instead of underline or dash characters to separate words of a single keyword
:arrow_forward: `base recalibration` (_not_: `base-recalibration`)
- for abbreviations: the full term should be included as well
:arrow_forward: `AMP, antimicrobial peptides`
- not for widely known terms
:arrow_forward: `DNA`, `RNA`
- file formats in lower case
:arrow_forward: `bam` (_not_: `BAM`)
- try to choose keywords that describe the tool and are not too broad
:arrow_forward: nothing like `density`, `family`
- review open branches
- close merged branches (Simon) :heavy_check_mark:
- close stale branches (when closing stale issues/PRs)
- move all issues/PRs with `hackathon2023` to the this year's hackathon project board (-> springclean_hack group)