Port sarek subworkflows to nf-core/modules
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 429
- Forks
- 1.1k
- Avg merge
- 1d 6h
- Merged PRs (30d)
- 153
Description
Please convert each of this as an issue when you start working on one.
(That can be done by clicking on the circle dot ⊙ at the end of the line in the list below, hover on a list item to see it)
And label it with the appropriate pipeline label (ie :sarek).
Note that a subworkflow can be useful for several pipelines.
I know for sure that some of these might and will be useful for at least raredisease, rnavar, variantcatalogue...
The names for the subworfklows in this issue are copy/paste from sarek, refer to #2157 to improve naming
And please update name by editing either this issue or the newly created
- new subworkflow alignment_to_fastq
- #6430
- new subworkflow cram_qc
- new subworkflow merge_index_bam
- new subworkflow merge_index_cram
- #5187
- new subworkflow vcf_qc
- #6090
- new subworkflow annotation/snpeff
- new subworkflow gatk4/joint_germline_variant_calling
- #2161
- #2163
- new subworkflow gatk4/markduplicates_spark
- new subworkflow gatk4/prepare_recalibration
- new subworkflow gatk4/prepare_recalibration_spark
- #6096
- new subworkflow gatk4/recalibrate_spark
- new subworkflow gatk4/single_sample_germline_variant_calling
- new subworkflow gatk4/tumor_normal_somatic_variant_calling
- new subworkflow gatk4/tumor_only_somatic_variant_calling
- new subworkflow variantcalling/ascat
- new subworkflow variantcalling/controlfreec/somatic
- new subworkflow variantcalling/controlfreec/tumoronly
- #2184
- #2215
- new subworkflow variantcalling/haplotypecaller
- new subworkflow variantcalling/manta/germline
- #5279
- new subworkflow variantcalling/manta/tumoronly
- new subworkflow variantcalling/mpileup
- new subworkflow variantcalling/strelka/single
- #6091
- new subworkflow variantcalling/tiddit/single
- new subworkflow variantcalling/tiddit/somatic
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 selecting one unchecked subworkflow from the checklist and read #2157 for the naming guidance. Create a separate issue using the circle control, apply the sarek label, and update the name if needed; completion means that selected subworkflow has been ported to nf-core/modules.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100