Index of values

FreeBayes' bamleftalign utility, which left-normalizes indels.

Transform a value of type Input.t into a list of BAMs.

Compute the base-path used by the EDSL.save function.

Optimized version of bwa-mem.

Example: call "gunzip <list of fastq.gz files> > some_name_cat.fastq".

Run delly2 on a tumor/normal sample.

Create a fastq_reads workflow_node from one or two single_file workflow_node(s).

This functions guesses whether to use fastq or fastq_gz given the file name extension.

Transform a value of type Input.t into a pipeline returning FASTQ data, providing the necessary intermediary steps.

Call the FASTQC tool (the result is an output directory custom to the tool).

Current Git commit (if avaiable at build-time)

Current result of "git describe" (if avaiable at build-time)

What to do with input files: copy or link them to the work directory, or do nothing.

Decrlare an URL as a input to a a pipeline.

Biokepi machine used by the TTFI workflow.

Whether or not to scatter-gather the indel-realigner results.

Input a file containing HLA allelles for Topiary

Directory where `save` files will end up.

Run a program that does not use much memory, runs on one core, and needs the internet.

Run a program that does not use much memory and runs on one core.

Sambamba's view filter tool, used to filter down a BAM to one with reads matching some predicate (filter language at https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax).

Tag a product of the EDSL as “interesting to be saved” (the meaning is implementation dependent; when compiling to a Ketrew workflow this means copying the file(s) to another directory.

A stream processor, for this purpose, is a program that runs on one core and does not grow in memory arbitrarily.

Make a filename-compliant string out of a region specification.

This is used to opacify the type of the expression.

Make a new bam sharing most of the metadata.

Concatenate VCF files.

Call a command on a list of ~vcfs to produce a given ~final_vcf (hence the n-to-1 naming).

Sort a VCF file by choromosome position (it uses "vcf-sort" which itself relies on the "sort" unix tool having the "--version-sort" option).

Official version string of the current build

Directory where all work product done by the TTFI end up.