Port sarek subworkflows to nf-core/modules

[maxulysse]

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

[scorreard]

Here is the documentation to add new modules : https://nf-co.re/developers/modules#writing-a-new-module-reference

[matthdsm]

@maxulysse , which one is the meta workflow with the aligners?