Prepare EMASE Pipeline ReadMe

Prepare-EMASE Input Files Documentation

Prepare-EMASE Pipeline (--workflow prepare_emase)

•   Step 1: Prepare EMASE reference   
•   Step 2: Prepare final transcript lists used in EMASE and also GBRS  

Prepare-EMASE Flowchart

flowchart TD
    p0[EMASE_PREPARE_EMASE]
    p1[BOWTIE_BUILD]
    p2[CLEAN_TRANSCRIPT_LISTS]

    o1([EMASE Input Files]):::output
    o2([Multiway Bowtie Reference]):::output
    o3([Transcript List for EMASE Input]):::output

    p0 --> p1
    p0 --> p2
    p0 --> o1
    p1 --> o2
    p2 --> o3


classDef output fill:#90aaff,stroke:#6c8eff,stroke-width:2px,color:#000000

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Parameters for Prepare-EMASE Pipeline

• --pubdir

  • Default: /<PATH>
  • Comment: The directory that the saved outputs will be stored.

• -w

  • Default: /<PATH>
  • Comment: The directory that all intermediary files and nextflow processes utilize. This directory can become quite large. This should be a location on /fastscratch or other directory with ample storage.

• --genome_file_list

  • Default: /<PATH> OR /<PATH>,/<PATH/,...
  • Comment: A comma separated list of FASTA genome file(s) for use hybrid genome construction (e.g., genome1.fa OR genome1.fa,genome2.fa,...). NOTE: FASTA AND GTF MUST BE IN THE SAME ORDER.

• --gtf_file_list

  • Default: /<PATH> OR /<PATH>,/<PATH/,...
  • Comment: A comma separated list of GTF files corresponding to the genomes for use hybrid transcriptome construction (e.g., genome1.gtf OR genome1.gtf,genome2.gtf,...). NOTE: GTF AND FASTA MUST BE IN THE SAME ORDER.

• --haplotype_list

  • Default: <comma,delim,string>
  • Comment: A list of haplotype names corresponding to genomes used in hybrid genome construction (e.g., 'A,B,C,D,E,F,G,H'). These names are appended to transcript IDs (e.g., ENMST00000042_A). NOTE: HAPLOTYPE LIST MUST BE IN THE SAME ORDER AS FASTA AND GTF FILES.

Pipeline Default Outputs

NOTE: * Represents a wild card that is a placeholder for values that will be filled by input file names and/or parameters when the pipeline is run.

Naming Convention	Description
prepare_emase_report.html	Nextflow autogenerated report
trace.txt	Nextflow trace of processes
*/emase/emase.pooled.transcripts.fa	Pooled transcripts in fasta format for all transcripts and haplotypes
*/emase/emase.gene2transcripts.tsv	Gene to transcript ID mapping in tab delimited format
*/emase/bowtie/*.ebwt	Bowtie index files required for mapping
*/emase/emase.fullTranscripts.info	The complete list of transcripts included in the bowtie index, and other files
*/emase/*.pooled.fullTranscripts.info	The complete list of transcripts, and transcript lengths for all haplotypes.

Pipeline Options Outputs

There are no optional outputs for this workflow.