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
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 leastraredisease
,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