Usage

Calling pipemake without any arguments or with the help flags will display the currently available pipelines (see Currently Available Pipelines):

pipemake

Once a pipeline has been selected, you may view the pipeline’s arguments by simply adding the pipeline name to the command.

For example, to view the arguments for the trim-fastqs pipeline, you would use the following command:

pipemake trim-fastqs

This would display the following information:

error: one of the arguments --fastq-wildcard --fastq-table --paired-end-sra --single-end-sra is required

usage: pipemake trim-fastqs (--fastq-wildcard FASTQ_WILDCARD | --fastq-table FASTQ_TABLE | --paired-end-sra PAIRED_END_SRA | --single-end-sra SINGLE_END_SRA)
                            [--fastq-copy-method {symbolic_link,copy}]
                            [--min-length MIN_LENGTH]
                            [--cut-front]
                            [--cut-tail]
                            [--cut-right]
                            [--workflow-dir WORKFLOW_DIR]
                            [--scale-threads SCALE_THREADS]
                            [--scale-mem SCALE_MEM]
                            [--resource-yml]
                            [--singularity-dir SINGULARITY_DIR]
                            [--no-overwrite]
                            [-h]

trim-fastqs required arguments:
--fastq-wildcard FASTQ_WILDCARD
                        Wildcard statement to represent FASTQs (supported wildcards: samples, reads)
--fastq-table FASTQ_TABLE
                        Table with sample and FASTQs filenames (supported wildcards: samples, reads)
--paired-end-sra PAIRED_END_SRA
                        Table with SRA accession numbers for paired-end reads (supported wildcards: samples)
--single-end-sra SINGLE_END_SRA
                        Table with SRA accession numbers for single-end reads (supported wildcards: samples)

trim-fastqs optional arguments:
--fastq-copy-method {symbolic_link,copy}
                        Specifies if FASTQs should be copied or symbolically linked. (default: symbolic_link)
--min-length MIN_LENGTH
                        Minimum length of reads to keep (default: 50)
--cut-front           Trim from the front of the reads
--cut-tail            Trim from the tail of the reads
--cut-right           Trim the right side of the reads, starting from the 5' end
--workflow-dir WORKFLOW_DIR
                        Assign the workflow directory. If not provided a default will be used.
--scale-threads SCALE_THREADS
                        Scale the threads for each task
--scale-mem SCALE_MEM
                        Scale the memory (RAM) for each task
--resource-yml        Create a seperate resource yaml
--singularity-dir SINGULARITY_DIR
                        Assign different directory of singularity images
--no-overwrite        Do not overwrite existing files
-h, --help            show this help message and exit

You may notice that the arguments are divided into two categories: required and optional.

• required is the category that holds arguments required by the pipeline to operate

• optional is the category that holds optional arguments that modify the pipeline’s behavior.

For the trim-fastqs pipeline to operate, the user must provided either: --fastq-wildcard, --fastq-table, --paired-end-sra, or --single-end-sra argument.

• --fastq-wildcard is used to specify a wildcard statement that represents the FASTQ files

• --fastq-table is used to specify a table with sample and FASTQ filenames

• --paired-end-sra is used to specify a table with SRA accession numbers for paired-end reads

• --single-end-sra is used to specify a table with SRA accession numbers for single-end reads

For example, let’s examine the files within the example directory example/trim-fastqs:

test1_R1.fq.gz
test1_R2.fq.gz
test2_R1.fq.gz

As you can see, the directory contains:

• A set of paired-end FASTQ files: test1_R1.fq.gz, test1_R2.fq.gz

• A single-end FASTQ file: test2_R1.fq.gz.

Since these files share a similar naming convention, we can use the --fastq-wildcard argument to assign the files. To do this, we must use the supported wildcards as given in the help message: samples and reads. If you wanted to perform the trim-fastqs pipeline on these files, you may use the following command:

pipemake trim-fastqs --fastq-wildcard example/trim-fastqs/{samples}_{reads}.fq.gz --workflow-dir TrimTest

This would generate a snakemake workflow called TrimTest.

Note

A warning will be displayed if:

• The input files have inconsistent wildcard usage (such as using paired-end alongside single-end files).

• No singularity path was specified. Which may result in redundant singularity containers being downloaded.

The workflow directory contains all neccessary files to execute the trim-fastqs pipeline on the provided FASTQ samples: test1 and test2.

The workflow could then be executed using the following command:

cd TrimTest
snakemake --use-singularity --cores 4