Add workflow to merge VCFs #6
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Right now it just merges text files with cat until we get the structure of the workflow set.
Note that this doesn't let us specify an outfile name, which is not ideal. It looks like you can't scatter over a map in WDL 1.0, which is what we're required to use.
The workflow may or may not be working - the test data I'm using has flipped alleles because they were converted from plink, which uses major/minor instead of ref/alt. So we'll need to flip some alleles to match a reference using a fasta file.
Getting an error that bcftools is failing to create the index.
I think they are needed but bcftools is failing here for some reason...
As expected, bcftools merge did fail with an error because no index was found.
By default, bcftools index creates the index file in the same place as the vcf (I think). It looks like we don't have permission to write to the mounted directory, so we'll have to create it in the current working directory and then later specify that it is the index for a given vcf. (We'll get to that later - for now just trying to create the vcf.)
I had misread 1.9 for 1.19 and thought I was using a newer version of bcftools. Switch the docker image to bcftools 1.15, and use the --no-index option when calling bcftools merge. (Switching the docker image may let us use an index file in a different directory, too.)
It's not being created right now
File type should be determined automatically from the suffix.
I think ${output_prefix} evaulated to zero, so it was creating a
hidden file with the name .vcf.gz. Fix the syntax so WDL expands the
variable (instead of bash).
I think DRS may be changing how "basename" works here, so try setting the index file name using an input instead of creating it from the vcf file name. Not sure.
Just create them no matter what.
bcftools merge has other options, and I don't want to code them all as booleans. This way, users can specify any of the options they want without having to make them arguments to the workflow.
Otherwise, it shows up in the Terra interface even if it's not an input to the workflow itself, just the task.
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This workflow calls "bcftools merge" and creates a merged VCF from those input files. It can run in parallel for multiple sets of VCFs to combine.