Options - Oshlack/necklace GitHub Wiki

Usage

<path_to_necklace>/tools/bin/bpipe run [options] <path_to_necklace>/necklace.groovy <config_file>

Options

  • -n <arg> - the number of threads
  • -p de_novo_assembly_file="<file_name.fasta>" - Pass a de novo assembly fasta file to use instead of running Trinity.
  • -p genome_guided_assembly_file="<file_name.gtf>" - Pass a genome-guided assembly gtf file to use instead of running StringTie.
  • -p fastqInputFormat="<pattern>" - A pattern to describe the file naming of the gzipped fastq files, where the wildcard % is used to match the sample ID and * is used to match the paired end. For example a filename format such as "ExperimentID_SampleID_R1/2.fq.gz" could be specified with the pattern, "ExperimentID_Sample%_R*.fq.gz" Default: "%_*.gz" ie. the form: SampleName_ReadEnd.fastq/fq.gz
  • -p trinity_options="<options>" - This string will be passed as the options to Trinity. See Trinity documentation for full options. Default: "--max_memory 50G --normalize_reads --no_version_check --trimmomatic"
  • -p stringtie_options="<options>" - This string will be passed as the options to StringTie. See StringTie documentation for full options. Default: no options
  • -p stringtie_merge_options="<options>" - This string will be passed as the options to StringTie --merge. See StringTie documentation for full options. Default: no options
  • -p hisat2_options="<options>" - This string will be passed as the options to Hisat2. See Hisat2 documentation for full options. Default: no options
  • -p blat_options="<options>" - This string will be passed to blat, when the de novo assembly is aligned against the genomic superTranscripts. Default: "-minScore=200 -minIdentity=98".
  • -p blat_related_options="<options>" - This string will be passed to blat, when the de novo assembly is aligned against the related species. Default: "-t=dnax -q=prot -minScore=200 -maxIntron=0".
  • -p featurecount_gene_options="<options>" - This string will be passed to featureCounts when counting reads in genes. See featureCounts documentation for full options. Default: "--primary -p".
  • -p featurecount_block_options="<options>" - This string will be passed to featureCounts when counting reads in blocks. See featureCounts documentation for full options. Default: "--primary -p -fraction -O".
  • -r - create a html report of the running time for the pipeline.

All the options above beginning with '-p', can alternatively be specified in the configuration file (without the '-p'). Also see the variables specified at the top of necklace.groovy to see what is settable.

Bpipe commands

In addition to "run" bpipe has a number of useful command to check on and control jobs. Usage:

<path_to_necklace>/tools/bin/bpipe [command]

Useful commands:

  • run - run the pipeline!
  • test - print the next stage in the pipeline which will be run (without actually running it). This is useful for debugging
  • retry - reruns the pipeline using the same options as the previous run
  • test - print the next stage in the pipeline which will be run (without actually running it). This is useful for debugging
  • history - tells you previous bpipe commands you've run. This makes it easy to rerun the same command again
  • log - a log of all the info bpipe outputs to stdout. This can be useful for monitoring jobs which are running in the background.
  • stop - stop bpipe from running.

For a full list of bpipe commands and options type:

<path_to_necklace>/tools/bin/bpipe
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