genome_preparation

These processes can be executed independently of datassets, their parameters do not depend on the data but on the genome used in the analysis.

workflow

Steps

Merge FastA files

If provided and required, the FastA files in fasta path can be merged to provide a reference fasta file. Only used when fasta file is not already provided. Files in the directory should have a “fa” or “fasta” extension and be plain text.

workflow:L43 tools/cat

Make FastA index

If not provided by the fasta index file parameter, the fasta file will be indexed using samtools faidx.

workflow:L74 samtools/faidx

Merge GTF files

If provided and required, the GTF files in gtf path can be merged to provide the gtf file parameter. This is only used when gtf file is not already provided. Files in the directory should have a “gtf” extension and be plain text.

workflow:L106 tools/cat

Make GRanges object

Create a GRanges object using the gneome name, gtf file and fasta index file.

workflow:L137 R/GenomicRanges/convert_gtf_to_granges

Connect to biomaRt

Creates a mart object to connect to the organism and ensembl release for the genome.

workflow:L171 R/biomaRt/get_mart

Printable channels

These channels can be dumped to the output device using the `-dump-channels` Nextflow option with the workflow root tag and the channel tag, for example: genome_preparation:tasks.

Tag	Description
`:genome_parameters`	The genome parameters used by datasets in the project.
`:fasta_file.{to_make,to_skip}`	Genomes that provide `fasta path` but not `fasta file` or genomes that provide `fasta file` or lack `fasta path`.
`:fasta_file`	Parameters with `fasta file`.
`:fasta_index_file.{to_make,to_skip}`	Genomes that do/not provide `fasta index file`.
`:fasta_index_file`	Parameters with `fasta index file`.
`:gtf_file.{to_make,to_skip}`	Genomes that provide `gtf path` but not `gtf file` or genomes that provide `gtf file` or lack `gtf path`.
`:gtf_file`	Parameters with `gtf file`.
`:granges_file.{to_make,to_skip}`	Genomes that provide both `fasta index file` and `gtf file` will have a GRanges object created.
`:granges_file`	Parameters with GRanges object file.
`:mart_file.{to_make,to_skip}`	Genomes that provide an `ensembl release` will have a biomaRt connection created.
`:mart_file`	Channel of `mart` objects.
`:complete_genome_parameters`	Genome parameters with process output keys added.
`:result`	Channel containing all of the parameters with these new keys added.
`:tasks`	Each task’s output `task.yaml` files from the `task` channel.