DSL2 Planning
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DSL2
enhancement
- Dominant language
- Nextflow
- Stars
- 215
- Forks
- 91
- Avg merge
- 5m
- Merged PRs (30d)
- 1
Description
Whelp, I guess we have to tackle the bull.
First thoughts, we need to work out what nf-core/modules we would need, check what are already available and what we would have to write.
List based on currently used tools in eager DSL1:
- adapterremoval
- adapterremovalfixprefix (although honestly would rather drop this entirely
- bwa
- aln (+ sampe/samse)
- mem
- index
- picard [Note: all in GATK4? Drop for GATK4 instead?]
- CreateSequenceDictionary
- AddOrReplaceReadGroups
- MarkDuplicates
- samtools
- faidx
- fastq
- index
- merge
- flagstat
- view
- sort
- #925
- mpileup
- fastqc
- dedup
- angsd
- doCounts
- contamination
- circularmapper
- circulargenerator
- circularmapper
- gatk4 HaplotypeCaller
- gatk3.5
- UnifiedGenotyper
- RealignerTargetCreator
- IndelRealigner
- UnifiedGenotyper
- qualimap
- bamqc
-
vcf2genomeno one is using it.. - damageprofiler
- multiqc
- pmdtools
- bedtools
- #779
- sequencetools
- preseq
- c_curve
- lc_extrap(?) <- requested
- fastp
- bamutil
- trimBam
- mtnucratio
- kraken2
- freebayes
- sexdeterrmine (+ samtools depth)
- multivcfanalyzer
- hops
- MALT
- maltExtract + Posprocessing
- bowtie2
- build
- align
- eigenstratdatabasetools
- eingenstrat_snp_coverage (+ parse_snp_cov.py)
- mapdamage
- bbmap
- bbduk.sh
- cat (fastq lane merge)
- hostremoval_input_fastq
- endorspy
- filter_bam_fragment_length.py
- print_x_contamination.py
- kraken_parse.py
- mege_kraken_res.py
- bcftools
- stats
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the eager DSL1 tool list in the issue and checking nf-core/modules availability for the unchecked entries. Done means the DSL2 plan identifies which listed tools can use existing modules, which require new modules, and which should be dropped or replaced.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100