Parameters

Parameters

Those parameters would cover the setting from nextflow.config file .

• Parameters
  • Mandatory
  • Configuration
  • Optional
  • Detailed instruction of parameters
• Config

Mandatory

(plz configure those options in nextflow.config or docker.config file) .

Name	Example/Default value	Description
--reads	./*{1,2}.fq.gz	input raw paired reads
--designfile	FALSE	a txt file that stored experimental design information, plz see details from --designfile section above
--comparefile	FALSE	a txt file that stored experimental compare information, plz see details from --comparefile section above

Configuration

(paths to references, softwares and special environments. Only need to be set at the first time you run the pipeline) .

Name	Example/Default value	Description
--redir	/path/to/refdir	the folder containing all reference files and index
--genomefile	path/to/refdir/chr2.fa	Path to Fasta reference(required if not set in config file)
--gtffile/--bedfile/--annotationfile	path/to/refdir/hg38_gencode.txt	Different annotation files from GENCODE database for annotating circRNAs. e.g. [gencode.v25.annotation.gtf]/[gencode.v25.annotation.bed]/[hg38_gencode.txt]
--ciridir/--find_circdir/--mapsdir/--knifedir	/path/to/tools/directory	Home folder of ciri/find_circ/mapsplice/knife installed location

Optional

Name	Default value	Description
--starindex/--bowtie2index/--bwaindex/--segindex/--bowtieindex/--refmapsplice/--knifeindex	-	Path to STAR/bowtie2/segemehl/bowtie/bwa/mapsplice/knife index. If not set, the pipeline will create the index itself.
--singleEnd	false	specify that the reads are single ended
--merge	true	merge the different matrixes produce by different tools and draw the venn graph
--separate	false	annotate the results separately
--selectTools	1	specify which tools should be use. 1 for circexplorer2, 2 for ciri, 3 for find_circ, 4 for mapsplice, 5 for segemehl, 6 for knife. For example, you can set 1,2,3,4,5 for running five tools in the same time.
--outdir	./Result	the output directory of the results
--mRNA	path/to/gencode.rsem.fpkm_m6Astatus_11_29.mat	Path to the mRNA expression matrix. Only need to be set when you want to do the correlation.

Detailed instruction of parameters

• --reads

  suffix of your raw reads file. For example, *_{1,2}.fq.gz for paired end reads file sampleA_1.fq.gz and sampleA_2.fq.gz

• --outdir

  path to the result output directory

• --selectTools

  specify which tools should be use. 1 for circexplorer2, 2 for ciri, 3 for find_circ, 4 for mapsplice, 5 for segemehl, 6 for knife. For example, you can set --selectTools='1,2,3,4,5' for running five tools in the same time.

• --starindex

  path to the STAR index directory. To build the index, you can use the command such as STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/wqj/test/starindex --genomeFastaFiles /home/wqj/database/circleTest/1.genome/chrX.fa --sjdbGTFfile /home/wqj/database/circleTest/1.genome/gencode.v25.annotation.chrX.gtf --sjdbOverhang 149.

• --segindex

  path to the Segemehl index directory. To build the index, you can use the command such as ./segemehl.x -d hg19.fa -x hg18.idx.

• --bowtie2index

  path to the Bowtie2 index directory. To build the index, you can use the command such as bowtie2-build -f ../chrX.fa chrX.

• --bowtieindex

  path to the Bowtie index directory. To build the index, you can use the command such as bowtie-build GENOME.fa GENOME.

• --bwaindex

  path to the BWA index directory. To build the index, you can use the command such as bwa index /home/wqj/database/circleTest/1.genome/chrX.fa -p genome.

• --knifeindex

  path to the KNIFE index directory. To build the index, you can follow the step in README.md in https://github.com/lindaszabo/KNIFE/tree/master/createJunctionIndex.

• --designfile

  design file

• --comparefile

  compare file

• --mRNA

  mRNA expression matrix file

• --gtffile

  gtf file for building your STAR index, running CIRI and Mapsplice, running annotation. For example, gencode.v25.annotation.gtf.

• --genomefile

  whole genome reference sequence in .fa format for running CIRCexplorer2, CIRI, Segemehl, Find_circ. For example, genome.fa.

• --annotationfile

  annotation file of genome in .txt format for running CIRCexplorer2. For example, hg38_gencode.txt.

• --bedfile

  annotation file of genome in .bed format for running CIRCexplorer2. For example, gencode.v25.annotation.bed.

• --refmapsplice

  path to the reference files for Mapsplice directory.

• --refdir

  path to the directory including all reference genome files and indexes files.

• --singleEnd

  true when using a single End reads input, default false

• --separate

  true when each selected pipelines producing its own results, default false

• --merge

  true when all results produced by selected pipelines merge together, default true

• --ciridir

  path to the CIRI scripts

• --find_circdir

  path to the Find_circ scripts

• --mapsdir

  path to the Mapsplice scripts

• --knifedir

  path to the KNIFE scripts

• --otherTools

  path to the in house R,Python,Java scripts

Config

As a nextflow-based analysis pipeline, CircPipe allow users edit configure file nextflow.config to set the index files and default file path parameters instead of typing them into the command line.

To configure, please go to params line, and set the following information of various file locations and system environment settings

params {

  container = 'likelet/circpipe:latest' // Container slug. Stable releases should specify release tag!

  //choose the tools
  separate = false
  merge = false
  selectTools = '6'

  //the necessary reference
  refdir = '/data1/wqj/database/data/testdata/Genome'
  annotationfile = "${params.refdir}/hg38_chr2_gencode.txt"
  genomefile = "${params.refdir}/chr2.fa"
  gtffile = "${params.refdir}/gencode_chr2.v25.annotation.gtf"
  bedfile = "${params.refdir}/gencode_chr2.v25.annotation.bed"
  refmapsplice = "${params.refdir}"
  mRNA = "/data1/wqj/database/data/testdata/gencode.rsem.fpkm_m6Astatus_11_29.mat"

  //reads files
  reads = "./*{1,2}.fq.gz"

  //the indexes for tools
  starindex = ""
  segindex = ""
  bowtie2index = ""
  bowtieindex = ""
  bwaindex = ""
  knifeindex = ""

  //the output directory
  outdir = './Result'

  //tools directory
  ciridir = '/home/wqj/tools/CIRI/bin/CIRI_v2.0.6'
  find_circdir = '/home/wqj/tools/find_circ'
  mapsdir = '/home/wqj/miniconda3/envs/tools_in_python3/bin'
  knifedir = '/home/wqj/tools/KNIFE'
  otherTools = "$baseDir/bin"

  //files of DE
  designfile='/data1/wqj/database/data/testdata/design.file'
  comparefile='/data1/wqj/database/data/testdata/compare.file'

  singleEnd = false

  email = '[email protected]'

  help = false
  igenomes_base = "./iGenomes"
  tracedir = "${params.outdir}/pipeline_info"
  clusterOptions = false
  awsqueue = false
  awsregion = 'eu-west-1'

}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

timeline {
  enabled = true
  file = "${params.tracedir}/nf-core/cirpipe_timeline.html"
}
report {
  enabled = true
  file = "${params.tracedir}/nf-core/cirpipe_report.html"
}
trace {
  enabled = true
  file = "${params.tracedir}/nf-core/cirpipe_trace.txt"
}
dag {
  enabled = true
  file = "${params.tracedir}/nf-core/cirpipe_dag.svg"
}

manifest {
  name = 'nf-core/cirpipe'
  author = 'Qi Zhao([email protected]), Qijin Wei([email protected])'
  homePage = 'https://github.com/likelet/cirpipe'
  description = 'cirRNA analysis pipe'
  mainScript = 'main.nf'
  nextflowVersion = '>=0.32.0'
  version = '1.0dev'
}