A repo for tools and workflows used by RAWG

This repo contains the RNASeq analysis tools we pakcaged in cwl script. Below is a list of all the tools we currently have and the input and output names for cwl scripts.

Mini documentation for each tools

The best effort has made to standardise input and output names but there is still plenty room for improvement. Suggestions and comments are very welcome!

Specify the inputs and outputs for each cwl script

• ballgown

  inputs:

  input_script: R ballgown script.
  tablemaker_output: directory of the tablemaker output
  metadata: metadata csv file.
  condition: string giving the condition of interest in the metadata columns

  outputs:

  DGE_res.csv
DTE_res.csv

• cuffdiff

  inputs:

  output: name for output directory
  threads: number of cores to use
  label: the factors of the condition of interest
  FDR: the FDR rate to which to label as significant, could default to 0.05.
  merged_gtf: merged gtf annotation file in gtf format
  condition1_files: cxb files of all samples for condition 1. cuffquant output
  condition2_files: cxb files of all samples for condition 2. cuffquant output

  outputs:

  output: names after inputs.output. directory containing all cuffdiff output files

  can add gene_exp.diff output only.

• cufflinks

  inputs:

  gtf: annotation file in gtf format
  output: name for output directory
  threads: number of threads to use.
  bam: bam file

  outputs:

  output: named after output_dir. directory with all cufflink file outputs
  transcripts.gtf

• cuffmerge

  inputs:

  output: string stating the output directory name
  gtf: annotation file in gtf format
  threads: number of threads to use.
  fasta: fasta file used in indexing
  cufflinks_output: transcripts.gtf files generated by cufflinks

  outputs:

  output: output directory named after input.output
  merged.gtf

• cuffnorm

  inputs: output: name for output directory
  threads: number of threads to use.
  merged_gtf: merged gtf annotation file in gtf format
  condition1_files: cxb files of all samples for condition 1. cuffquant output
  condition2_files: cxb files of all samples for condition 2. cuffquant output

  outputs:

  output: named after inputs.output. file contained normalised gene count matrix

• cuffquant

  inputs:

  output: name for output directory
  threads: number of threads to use.
  merged_gtf: merged gtf annotation file in gtf format
  bam: bam file

  outputs:

  output: named after inputs.output. Directory containing all quant files
  abundances.cxb

• DESeq2

  inputs: input_script: R DESeq2 script.
  count_matrix: gene count matrix file
  metadata: metadata csv file.

  outputs:

  DGE_results.csv

• DEXSeq

  inputs:

  input_script: R DEXSeq script
  count_matrix: exon count matrix file
  gff: directory containing gff file from htseq prepare
  metadata: metadata csv file.
  threads: number of threads to use

  outputs:

  DEE_results.csv

• edger

  inputs:

  input_script: R edger script
  condition: string giving the condition of interest in the metadata columns
  count_matrix: gene counts matrix
  metadata: metadata csv file.

  outputs:

  DGE_res.csv

• featurecounts

  inputs:

  input_script: R featurecounts script
  bam_files: all bam files
  gtf: annotation in ftd format
  threads: number of threads to use.
  metadata: used to see the libType of each sample.

  outputs: gene_count_matrix.csv

• fgsea

  inputs:

  input_script: R fgsea input_script
  de_results: DGE res file
  gene_set: file containing gene set information in long form.

  ouputs: gsea_res.csv

• hisat2_align

  inputs:

  threads: number of threads
  index_directory: path to hisat2 index
  first_pair: first fastq file
  second_pair: second fastq file
  output: output name
  XSTag: Tag to use ("--dta" or "--dta-cufflinks")

  outputs:

  hisat2_align_out: everything sam_output: sam files

• hisat2_build

  inputs:

  fasta: fasta file
  threads: number of threads to use.
  output: name to use for output

  outputs:

  output: samfile with a basename given from inputs.output
  log

• htseq_count

  inputs:

  input_script: python htseq_count script
  pairedend: logical
  stranded: logical
  input_format: bam or sam
  sorted_by: pos
  gff: gff file from htseq_annotation
  bam: bam or sam file
  outname: name for outfile

  outputs:

  outname: named after input.ouput

• htseq_prepare

  inputs:

  input_script: python input script
  gtf: gtf annotation file
  gff_name: name for gff output

  outputs:

  gff_name: gff file named after inputs.gff_name

• hypergeo

  inputs:

  input_script: R HyperGeo_Script script
  de_res: DGE res file
  gene_set: file containing gene set information in long form.

  outputs:

  hypergeo_res.csv

• miso_index

  inputs:

  gtf: gtf file
  output: output name for output directory

  outputs:

  index_dir: output directory named after inputs.index_dir

• miso_run

  inputs:

  threads: number of threads to use
  lib_type: pairedend or not

  change to pairedend or change all other to lib_type

  index_directory: Directory from miso_index output
  bam: bam file
  read_len: read length
  gtf: gtf file
  min_exon_size: minimum exon size to use
  output: output name

  outputs:

  out_dir: directory named after inputs.out_dir

• prepDE

  inputs:

  input_script: python prepDE script
  stringtie_out: gtf files from stringtie

  outputs:

  gene_count_matrix.csv transcript_count_matrix.csv

• salmon_count

  inputs:

  input_script: R count script
  gtf: annotation file in gtf format
  metadata: metadata.csv
  quant_results: directory with subdirectorys of outputs from salmon_quant

  outputs:

  gene_abundance_matrix.csv
gene_count_matrix.csv * this one used for DGE analysis e.g. DESeq2
  gene_length_matrix.csv

• salmon_index

  inputs:

  fasta: fasta files
  index_type: 2 different type of running "fmd" or "quasi"
  threads: number of threads to use
  output: directory output name

  outputs:

  index_name: output directory with name inputs.index_name

• salmon_quant

  inputs:

  index_directory: directory of salmon index
  threads: number of threads to use
  output: output name
  first_end_fastq: if paired end. first pair fastq file
  second_end_fastq if paired end. second pair fastq file
  single_fastq: if single end. single fastq file

  outputs:

  out_dir: Directory with name of inputs.out_dir

• samtools

  inputs:

  action: samtools command (default in sort)
  sortby: how to sort the bam file
  threads: how many threads to use (total - 1), it is additional
  samfile: sam file
  outfilename: ouutput file name

  outputs:

  outfilename: bam file with name inputs.outfilename

• STAR_index

  inputs:

  threads: number of threads
  Mode: how to run STAR (use genomeGenerate)
  output: directory name to use
  fasta: fasta files
  gtf: gtf file

  outputs:

  index_out: index files

• STAR_readmap

  inputs:

  threads: number of threads to use
  genomeDir: directory name to use
  readFilesIn: fastq files
  outFileNamePrefix: output name for directory

  outputs:

  star_read_out: every output file sam_output: sam file

• stringtie

  inputs:

  bam: bam file
  threads: number of threads to use.
  gtf: gtf file
  output: output name for file

  outputs:

  outfilename: output file name with name inputs.outfilename

• tablemaker

  inputs:

  threads: number of threads to use.
  merged_gtf: merged gtf from cuffmerge
  bam: bam files to use
  output: output name for directory.

  outputs:

  output: Directory with name inputs.outputs