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## 🚀 Pipeline Documentation 🚀
_16th-18th March 2022_
This file: [https://hackmd.io/@nf-core/BylxH-Ygq/edit](https://hackmd.io/@nf-core/BylxH-Ygq/edit)
<img src="https://openmoji.org/data/color/svg/E040.svg" width=50> @nf-core / <img src="https://openmoji.org/data/color/svg/E045.svg" width=50> @nf-core
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# Pipeline Team
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# Tasks Ideas: Devs
- Review docs for anything missing (usage, output, JSON schema)
- Make workflow diagrams and annotated output doc images
- Write step-by-step pipeline tutorial (how to build a command)
- Update all long-form pipeline parameter help messages
- Describe which parameter of the _actual_ tool is being updated
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# Tasks Ideas: Volunteers
General:
- Check issues on project board for missing docs!
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# Remember
- Add yourself to Team Members
- Assign yourself on issues on the [project board](https://github.com/orgs/nf-core/projects/27/views/5)
- Post your progress here! One slide per pipeline
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# Team Members
* [James Fellows Yates](https://github.com/jfy133) (eager, funcscan, taxprofiler)
* [Maxime Garcia](https://github.com/maxulysse) ([sarek](https://github.com/nf-core/sarek))
* Mei Wu (raredisease)
* Anders Jemt (raredisease)
* Gwenna Breton (raredisease)
* Annick Renevey (rnafusion)
* Subazini Thankaswamy Kosalai (raredisease)
* [James Chela](https://github.com/chelauk) (sarek)
* Friederike Hanssen (sarek)
* Nick Smith (Sarek)
* [Jasmin Frangenberg](https://github.com/jasmezz) (funcscan)
* [Moritz E. Beber](https://github.com/Midnighter) (funcscan, taxprofiler)
* [Louisa Perelo](https://github.com/louperelo) (funcscan)
* [Anan Ibrahim](https://github.com/Darcy220606) (funcscan)
* Sarah Guinchard (rnaseq)
* Paul Cantalupo
* [Maxime Borry](https://github.com/maxibor)
* [Alexander Peltzer](https://github.com/apeltzer)
* Xiang-Jun Lu
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# Day One
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# eager
- [#835](https://github.com/nf-core/eager/issues/835) Fixed PreSeq params help message [JAFY]
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# raredisease
- [#121](https://github.com/nf-core/raredisease/issues/121) Example usage [name=Mei Wu] :heavy_check_mark:
- [#128](https://github.com/nf-core/raredisease/issues/128) docs: credits [name=Mei Wu] :heavy_check_mark:
- [#118](https://github.com/nf-core/raredisease/issues/118) Collaboration: clarify mtDNA subworkflow [name=STK,GB] :heavy_check_mark:
- [#117](https://github.com/nf-core/raredisease/issues/117) In progress flowchart [name=GB,STK] :heavy_check_mark:
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# rnafusion
- [#209](https://github.com/nf-core/rnafusion/issues/209) Update documentation [name=AR]
- README sanitized
- TODOs checked
- Initial flowchart plans
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# sarek
- [#502](https://github.com/nf-core/sarek/issues/502) Update nextflow.json [name=MUG]
- [#503](https://github.com/nf-core/sarek/issues/503) Tube Map [name=CJ,NS]
- started on tube map for sarek prepare indices subworkflow
- started on tube map for sarek basic mapping
- [#504](https://github.com/nf-core/sarek/issues/504) Update usage.md [name=FH]
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# scrnaseq
- [#50](https://github.com/nf-core/scrnaseq/issues/50) Checked for missing modules [name=AP]
- [#92](https://github.com/nf-core/scrnaseq/issues/92) Discussion on new Samplesheet Format [name=GG,GS,AP]
- [#469](https://github.com/nf-core/test-datasets#469) Added new Samplesheet format to test-datasets [name=AP]
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# funcscan
- Project Meeting
- Reviewed open PRs [name=JAFY, JF, LP]
- resolving conflicts of the new template v2.3 [name=MEB]
- [#33](https://github.com/nf-core/funcscan/issues/33) Started output documentation [name=LP]
- [#30](https://github.com/nf-core/funcscan/issues/30) Started updating work-diagram [name=AI]
- assemble info of all inputs/outputs for all modules
- switched to metro style, still need colour scheme
- [#31](https://github.com/nf-core/funcscan/issues/31) Started parameters documentation [name=JF]
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# taxprofiler
- Project Meeting
- Started pipeline diagram [name= JAFY]
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# rnaseq
- Added a few issues from gathered input [name= SG]
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# mag
- [#161](https://github.com/nf-core/mag/issues/161) finished it and created [PR](https://github.com/nf-core/mag/pull/282) [name= Paul C]
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# Day Two
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# rnaseq
- [#788] Added an up-to-date Singularity installation tutorial since the one on Sylabs' website uses an outdated GO compiler version [name= SG]
- [#787] Clarified when it's a bad idea to use conda [name= SG]
- Made the same update to the nf-core pipeline template for future tools [name = SG]
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# eager
- Updated MultiQC config to rename some General Stats column headers [name= JAFY]
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# raredisease
- [#132](https://github.com/nf-core/raredisease/issues/132) schema_param: local_genomes [name=Mei Wu] :heavy_check_mark:
- [#134] (https://github.com/nf-core/raredisease/issues/134) Step by step tutorial -Mitochondria pipeline [name=Subazini TK]
- Will discuss flow chart
- integrate mito workflow
- [#133](https://github.com/nf-core/raredisease/issues/133) Organize schema and hide params with defaults for specific steps (e.g. calling step)
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# fetchNGS
- [#80](https://github.com/nf-core/fetchngs/pull/80) Add troubleshooting section and FTP alternative docs [name= MB]
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# kmermaid
- [#148](https://github.com/nf-core/kmermaid/pull/148) Update pipeline schema and default parameters values [name= MB]
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# funcscan
- Remaining PRs merged (incl. new template), waiting for tests to succeed [name= JAFY, JF]
- Continue output documentation (finished second tool description - still five to go) [name= LP]
- Continue graphical pipeline diagram [name= AI]
- Fought with broken dependencies of broken tools 😭 [name=JAFY]
- Continue parameters documentation [name= JF]
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# mag
- Fixed software version reporting issue in a PR [name=JAFY]
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# taxprofiler
- [#20](https://github.com/nf-core/taxprofiler/issues/20) Started adding support for nanopore data
- [#3](https://github.com/nf-core/taxprofiler/issues/3) Started creating new kaiju module
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# Day Three
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# raredisease
- [#133](https://github.com/nf-core/raredisease/issues/133) Organize schema and hide params with defaults for specific steps (e.g. calling step)
- [137](https://github.com/nf-core/raredisease/issues/137) Update resource request in usage
- [126](https://github.com/nf-core/raredisease/issues/126) Describe samplesheet [name=AJ]:heavy_check_mark:
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# viralrecon
- Draft pipeline diagram started [name=X-JL]
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# rnaseq
- [#762](https://github.com/nf-core/rnaseq/issues/762) Added a warning about --skip_bbsplit staying true by default even if you provide files to the other bbsplit parameters [name=SG]
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# rnaseq
- [#69](https://github.com/nf-core/rnaseq/issues/69) Added a link to QCfail to help with the interpretation of fastQC output and a warning about the output of SortMeRNA. Concluded it would be next to impossible to provide good/bad output examples for all tools since this can vary a lot depending on the experimental design [name=SG]
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# rnaseq
- Started working on a metro map for the pipeline but won't be done in time for chekout 🐌 [name=SG]
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# sarek
- [#502](https://github.com/nf-core/sarek/issues/502) Update nextflow.json [name=MUG]
- [#504](https://github.com/nf-core/sarek/issues/504) Update usage.md, finished samplesheet updates, Tutorials WIP [name=FH]
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# sarek
- [#503](https://github.com/nf-core/sarek/issues/503) Tube Map [name=CJ,NS,MUG]
- Started on:
- prepare indices subworkflow
- basic mapping -> basic preprocessing
- Plan for overall combination of subworkflows maps
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# scrnaseq
- Working on producing appropriate test-data for alevin-fry workflow to test required modules [name=AP]
- Using tutorial by alevin-fry team to generate what we need
- Will upload RAD file to testdata once done - can run quant afterwards
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# taxprofiler
- Started completing test-data & documenting how generated [name=JAFY]
- Broke UNTAR/UNZIP in loads of modules [name=JAFY]
- [#23](https://github.com/nf-core/taxprofiler/issues/23) Taxprofiler can take Nanopore reads (fastq.gz) as input through sample sheet [name=LM]:heavy_check_mark:
- [#26](https://github.com/nf-core/taxprofiler/pull/26) Perform fastqc on nanopore reads before trimming [name=LM]:heavy_check_mark:
- [#1410](https://github.com/nf-core/modules/pull/1410) Centrifuge module [name=SS]:heavy_check_mark:
- [#1398](https://github.com/nf-core/modules/issues/1398) Kaiju module [name=TN]
- [#1403](https://github.com/nf-core/modules/issues/1403) MetaMaps module [name=HO]
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# funscan
- More f*ckin' deepARG fixes[name=JAFY]
- ❤️🙏🙌 [name=JF]
- Pipeline workflow optimization [name=AI, JF]
- [#37](https://github.com/nf-core/funcscan/pull/37) Metro workflow draft: [name=AI] 
- Parameters documentation [name=JF]
- Output documentation [name=LP]
- First commit finiiished :heavy_check_mark:, PR coming in!
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# rnafusion
- README/CITATIONS/schema: finished
- Ongoing: usage/output
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# pangenome
- Documentation is a work in progress https://github.com/pangenome/pggb/pull/168. I am first adding documentation to PGGB. Then, I can copy it to the actual cluster-scalable nf-core pangenome pipeline.
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