Usage

Quick Start

Users can run a demonstration workflow by running:

$ raft.py run-demo -w rna-alns-transcript-counts

This will:

Create a project named demo-rna-alns-transcript-counts in ./raft/projects
Download the required RAFT modules
Download the demo references, FASTQS, and manifest
Run the project’s workflow

Outputs can be found in ./raft/projects/demo-rna-alns-transcript-counts/outputs. More information about output directory organization can be found in Outputs.

Finding Off-the-shelf Workflows

RAFT supports a variety of workflows. Users can list the currently available workflows by running:

$ raft.py available-workflows

Each workflow supports a variety of species (human or mouse) as well as a variety of starting inputs. Users can find which species and inputs are supported for each workflow by running:

$ raft.py available-workflows -w <WORKFLOW_NAME>

For example:

$ raft.py available-workflows -w gene-fusions

produces the output

Listing all versions of gene-fusions workflow.
--------------------------------------------------------------------------------
Workflow        Species Input
gene-fusions    human   junctions
gene-fusions    human   bams
gene-fusions    human   fastqs
--------------------------------------------------------------------------------

Users can find detailed information about each workflow by running:

$ raft.py available-workflows -w <WORKFLOW_NAME> -s <SPECIES> -i <INPUT_TYPE>

For example:

$ raft.py available-workflows -w gene-fusions -i fastqs

produces the output

Details for human gene-fusions workflow starting from fastqs.
--------------------------------------------------------------------------------
Default parameters:
-------------------
Parameter                       Value
---------                       -----
fq_trim_tool                    fastp
fq_trim_tool_parameters         None (tool defaults)
fusion_tool                     starfusion
fusion_tool_parameters          starfusion: --examine_coding_effect
fusion_ref                      starfusion: ${params.ref_dir}/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play
dna_ref                         ${params.ref_dir}/Homo_sapiens_assembly38.fasta
gtf                             None
--------------------------------------------------------------------------------
Workflow steps:
---------------
utilities::parse_manifest
fusion::manifest_to_fusions
--------------------------------------------------------------------------------
Alternate tools:
----------------
Parameter                       Alternate tools
---------                       ---------------
fq_trim_tool                    trim_galore,trimmomatic,fastp
fusion_tool                     fusioncatcher,jstarfusion,starfusion,arriba

Running Off-the-shelf Workflows

Users can run an off-the-shelf workflow with their own manifest by running:

$ raft.py run-ots -p <PROJECT_ID> \
                  -w <WORKFLOW_NAME> \
                  -s <SPECIES> \
                  -i <INPUT_TYPE> \
                  -m </PATH/TO/MANIFEST>

For example:

$ raft.py run-ots -p my-project-tx-counts-01JAN2024 \
                  -w rna-alns-transript-counts \
                  -s human \
                  -i fastqs \
                  -m </PATH/TO/MANIFEST>

Note that raft.py run-ots assumes human samples and FASTQs inputs, so the the above command is equivilant to the following:

$ raft.py run-ots -p my-project-tx-counts-01JAN2024 \
                  -w rna-alns-transript-counts \
                  -m </PATH/TO/MANIFEST>

Running Off-the-shelf Workflows with User-defined Parameters

Users can run an off-the-shelf workflow with their preferred tools and tool parameters using the raft.py -up/--user-params argument. This argument can be specified any number of times. For example, if a user wants to run the rna-alns-transcript-counts workflow with their own manifest, but with trim_galore instead of fastp, then they can run:

$ raft.py run-ots -p my-project-tx-counts-01JAN2024 \
                  -w rna-alns-transript-counts \
                  -m </PATH/TO/MANIFEST>  \
                  -up fq_trim_tool=fastp \
                  -up fq_trim_tool_parameters=fastp:'--paired'

Users may specify multiple tools and parameters for each of multiple tools using the following syntax:

$ raft.py run-ots -p ... \
                  ... \
                  -up fq_trim_tool=tool1,tool2 \
                  -up fq_trim_tool_parameters=tool1:'--params --for --tool 1',\
                                              tool2:'--params --for --tool 2'

Generally speaking, it is only recommended to use multiple tools for the last modifying step of the workflow. For example, the gene-fusions workflow for humans starting from FASTQs allow both fq_trim_tool and fusion_tool to be specified. fusion_tool generates the ultimate outputs from the workflow and thus users can specify multiple fusion_tool tools (e.g. fusion_tool=starfusion,arriba). fq_trim_tool, however, is upstream of fusion calling and users should only specify a single tool for fq_trim_tool.