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Port sarek subworkflows to nf-core/modules
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
- [ ] new subworkflow bam_to_cram
- [ ] new subworkflow cram_qc
- [ ] new subworkflow merge_index_bam
- [ ] new subworkflow merge_index_cram
- [x] #5187
- [ ] new subworkflow vcf_qc
- [ ] new subworkflow annotation/ensemblvep
- [ ] new subworkflow annotation/snpeff
- [ ] new subworkflow gatk4/joint_germline_variant_calling
- [x] #2161
- [ ] #2163
- [ ] new subworkflow gatk4/markduplicates_spark
- [ ] new subworkflow gatk4/prepare_recalibration
- [ ] new subworkflow gatk4/prepare_recalibration_spark
- [ ] new subworkflow gatk4/recalibrate
- [ ] 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
- [ ] new subworkflow variantcalling/strelka/somatic
- [ ] new subworkflow variantcalling/tiddit/single
- [ ] new subworkflow variantcalling/tiddit/somatic
Here is the documentation to add new modules : https://nf-co.re/developers/modules#writing-a-new-module-reference
@maxulysse , which one is the meta workflow with the aligners?