---
# System prepended metadata

title: spring cleaning march 2023 modules
tags: [' modules', ' maintainers', spring cleaning, ' meeting notes']

---

---
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)