Description of feature
Categorization of the workflow at the process level with the corresponding modules needed to port to 'DSL2'. Once the modules have been created, I can place more shape on this in terms of subworkflows.
N.B: please checkout new branches for individual features and push to the DSL2 branch, not dev.
Input files
Currently, circRNA takes as input a samplesheet.csv file and a phenotype.csv file. Functions already exist to check these files, all that is needed is to place these in an input_check.nf local subworkflow.
I would like to incorporate strandedness like other nf-core workflows. Will check which circRNA quantification tools have a parameter denoting strandedness.
Pre-processing
The workflow takes as input fastq or bam files (which are converted to fastq using picard SamToFastq) and performs FastQC on the raw reads prior to trimming using BBDUK. The trimmed reads are then checked using FastQC again and placed in channels for downstream analyses.
circRNA Discovery
Several tools utilize the same aligner, there will be duplicates here.
CIRIquant
CIRCexplorer2
circRNA_finder
DCC
DCC maps paired-end reads jointly and separately using STAR 2 pass mode. The goal is to generate chimeric.junction.out files from joint STAR mapping and individual read 1 and read 2 STAR mapping.
find_circ
Mapsplice
Segemehl
Custom scripts to parse segemehl output, no need to create a module.
circRNA annotation
customized bash script to standardise the annotation outputs from the seven quantification tools.
circRNA FASTA sequence
customized bash script to generate the mature spliced sequence in FASTA format, and append the back-splice junction sequence for miRNA target prediction.
circRNA count matrix
consolidate the circRNAs called by multiple tools on a per sample basis, generate the count matrix.
miRNA target prediction
miRanda
TargetScan
custom script to amalgamate the results from both tools.
Differential expression
Custom R scripts for DESeq2 and CircTest, no need to create modules.
Description of feature
Categorization of the workflow at the process level with the corresponding modules needed to port to 'DSL2'. Once the modules have been created, I can place more shape on this in terms of subworkflows.
N.B: please checkout new branches for individual features and push to the
DSL2branch, notdev.Input files
Currently, circRNA takes as input a
samplesheet.csvfile and aphenotype.csvfile. Functions already exist to check these files, all that is needed is to place these in aninput_check.nflocal subworkflow.I would like to incorporate
strandednesslike other nf-core workflows. Will check which circRNA quantification tools have a parameter denoting strandedness.Pre-processing
The workflow takes as input
fastqorbamfiles (which are converted tofastqusingpicard SamToFastq) and performsFastQCon the raw reads prior to trimming usingBBDUK. The trimmed reads are then checked usingFastQCagain and placed in channels for downstream analyses.FastQCMultiQCBBDUKpicard/SamToFastq(I don't care if we drop this functionality.)circRNA Discovery
Several tools utilize the same aligner, there will be duplicates here.
CIRIquant
bwa indexhisat buildciriquantCIRCexplorer2
STAR genomegenerateSTAR align(2 Pass mode)circexplorer2 parsecircexplorer2 annotatecircRNA_finder
star genomegeneratestar align(2 Pass mode)circRNA_Finder(postProcessStarAlignment.plscript)DCC
DCC maps paired-end reads jointly and separately using STAR 2 pass mode. The goal is to generate
chimeric.junction.outfiles from joint STAR mapping and individual read 1 and read 2 STAR mapping.star genomegeneratestar align(2 Pass)dccfind_circ
bowtie2 buildbowtie2 alignfind_circ find_anchorsfind_circ find_circMapsplice
bowtie buildmapsplice aligncircexplorer2 parsecircexplorer2 annotateSegemehl
segemehl alignCustom scripts to parse
segemehloutput, no need to create a module.circRNA annotation
customized bash script to standardise the annotation outputs from the seven quantification tools.
circRNA FASTA sequence
customized bash script to generate the mature spliced sequence in FASTA format, and append the back-splice junction sequence for miRNA target prediction.
circRNA count matrix
consolidate the circRNAs called by multiple tools on a per sample basis, generate the count matrix.
miRNA target prediction
miRanda
mirandaTargetScan
targetscan. biocontainers #475custom script to amalgamate the results from both tools.
Differential expression
hisat buildhisat alignstringiteCustom R scripts for DESeq2 and CircTest, no need to create modules.