Type tree¶
Process types are listed alphabetically. Next to each type is
a list of processes of that type. Types are hierarchical, with
levels of hierarchy separated by colon “:”. The hierarchy defines
what is accepted on inputs. For instance, Expression (Cuffnorm)
process’ input is data:alignment:bam
. This means it also
accepts all subtypes (e.g., data:alignment:bam:bwasw
,
data:alignment:bam:bowtie1
and data:alignment:bam:tophat
).
We encourage the use of existing types in custom processes.
data:aggregator:expression
- Expression aggregatordata:alignment
- Abstract alignment processdata:alignment:bam:bowtie1
- Bowtie (Dicty)data:alignment:bam:bowtie2
- Bowtie2data:alignment:bam:bwaaln
- BWA ALNdata:alignment:bam:bwamem
- BWA MEMdata:alignment:bam:bwasw
- BWA SWdata:alignment:bam:bwatrim
- Align (BWA) and trim adaptersdata:alignment:bam:hisat2
- HISAT2data:alignment:bam:primary
- Bam splitdata:alignment:bam:secondary
- Secondary hybrid BAM filedata:alignment:bam:star
- STARdata:alignment:bam:subread
- Subreaddata:alignment:bam:upload
- BAM file, BAM file and indexdata:alignment:bam:vc
- Indel Realignment and Base Recalibrationdata:alignment:mr:walt
- WALTdata:annotation
- Abstract annotation processdata:annotation:cuffmerge
- Cuffmergedata:annotation:gff3
- GFF3 filedata:annotation:gtf
- Convert GFF3 to GTF, GTF filedata:archive:samples
- Archive samplesdata:archive:samples:amplicon
- Archive and make multi-sample report for amplicon datadata:bam:plot:bamliquidator
- Bamliquidatordata:bam:plot:bamplot
- Bamplotdata:bed
- Abstract bed process, BED filedata:chipseq:batch:macs2
- ChIP-seq (MACS2), ChIP-seq (MACS2-ROSE2)data:chipseq:callpeak:macs14
- MACS 1.4data:chipseq:callpeak:macs2
- MACS 2.0data:chipseq:genescore
- ChIP-Seq (Gene Score)data:chipseq:peakscore
- ChIP-Seq (Peak Score)data:chipseq:rose2
- ROSE2data:clustering:hierarchical:gene
- Hierarchical clustering of genesdata:clustering:hierarchical:sample
- Hierarchical clustering of samplesdata:coverage
- coverageBeddata:cufflinks:cufflinks
- Cufflinks 2.2data:cufflinks:cuffquant
- Cuffquant 2.2, Cuffquant resultsdata:cuffnorm
- Cuffnormdata:differentialexpression
- Abstract differential expression processdata:differentialexpression:cuffdiff
- Cuffdiff 2.2data:differentialexpression:deseq2
- DESeq2data:differentialexpression:edger
- edgeRdata:differentialexpression:upload
- Differential Expression (table)data:etc
- Expression Time Course, Expression time coursedata:expression
- Abstract expression process, Expression data, Expression data (Cuffnorm)data:expression:featurecounts
- featureCountsdata:expression:htseq:cpm
- HTSeq-count (CPM)data:expression:htseq:normalized
- HTSeq-count (TPM)data:expression:polya
- Dictyostelium expressionsdata:expression:rsem
- RSEMdata:expression:shrna2quant
- Quantify shRNA species using bowtie2data:expression:star
- Expression data (STAR)data:expressionset
- Expression matrixdata:expressionset:etc
- Merge Expressions (ETC)data:file
- BaseSpace filedata:gaf:2:0
- GAF filedata:geneset
- Gene set, Gene set (create)data:geneset:venn
- Gene set (create from Venn diagram)data:genome:fasta
- Genomedata:genomeindex:star
- STAR genome indexdata:goea
- GO Enrichment analysisdata:index:expression
- Gene expression indicesdata:index:salmon
- Salmon Indexdata:junctions:regtools
- Annotate novel splice junctions (regtools)data:mappability:bcm
- Mappability, Mappability infodata:masterfile:amplicon
- Custom master filedata:metabolicpathway
- Metabolic pathway filedata:multiplexed:qseq:paired
- Reads (QSEQ multiplexed, paired)data:multiplexed:qseq:single
- Reads (QSEQ multiplexed, single)data:multiqc
- MultiQCdata:ontology:obo
- OBO filedata:other:geo:chipseq
- Prepare GEO - ChIP-Seqdata:other:geo:rnaseq
- Prepare GEO - RNA-Seqdata:pca
- PCAdata:picard:coverage
- Picard CollectTargetedPcrMetricsdata:picard:coverage:upload
- Upload Picard CollectTargetedPcrMetricsdata:prepeakqc
- Pre-peakcall QCdata:reads:fastq:paired
- Convert files to reads (paired-end), FASTQ file (paired-end), SRA data (paired-end)data:reads:fastq:paired:bbduk
- BBDuk (paired-end)data:reads:fastq:paired:cutadapt
- Cutadapt (Diagenode CATS, paired-end), Cutadapt (paired-end)data:reads:fastq:paired:seqtk
- Subsample FASTQ (paired-end)data:reads:fastq:paired:trimmomatic
- Trimmomatic (paired-end)data:reads:fastq:single
- Convert files to reads (single-end), FASTQ file (single-end), SRA data (single-end)data:reads:fastq:single:bbduk
- BBDuk (single-end)data:reads:fastq:single:cutadapt
- Cutadapt (Diagenode CATS, single-end), Cutadapt (single-end)data:reads:fastq:single:seqtk
- Subsample FASTQ (single-end)data:reads:fastq:single:trimmomatic
- Trimmomatic (single-end)data:report:amplicon
- Amplicon reportdata:sam:header
- SAM headerdata:seq:nucleotide
- FASTA filedata:snpeff
- snpEffdata:snpeff:upload
- snpEffdata:spikeins
- Spike-ins quality controldata:sra
- SRA datadata:strandedness
- Detect library strandednessdata:test:disabled
- Test disabled inputsdata:test:fields
- Test basic fieldsdata:test:hidden
- Test hidden inputsdata:test:result
- Test select controler, Test sleep progressdata:variants:vcf
- VCF filedata:variants:vcf:chemut
- Variant calling (CheMut)data:variants:vcf:filtering
- Variant filtering (CheMut)data:variants:vcf:gatk:hc
- GATK3 (HaplotypeCaller), GATK4 (HaplotypeCaller)data:variants:vcf:lofreq
- LoFreq (call)data:varianttable:amplicon
- Amplicon tabledata:wgbs:hmr
- HMRdata:wgbs:methcounts
- methcountsdata:workflow:amplicon
- Accel Amplicon Pipelinedata:workflow:atacseq
- ATAC-Seqdata:workflow:chemut
- Chemical Mutagenesisdata:workflow:chipseq:macs2rose2
- MACS2 - ROSE2data:workflow:mirna
- miRNA pipelinedata:workflow:quant:featurecounts:paired
- BBDuk - STAR - FeatureCounts (3’ mRNA-Seq, paired-end)data:workflow:quant:featurecounts:single
- BBDuk - STAR - FeatureCounts (3’ mRNA-Seq, single-end), Cutadapt - STAR - FeatureCounts (3’ mRNA-Seq, single-end), Cutadapt - STAR - FeatureCounts - basic QC (3’ mRNA-Seq, single-end)data:workflow:rnaseq:corall
- Cutadapt - STAR - StringTie (Corall, paired-end), Cutadapt - STAR - StringTie (Corall, single-end)data:workflow:rnaseq:cuffquant
- RNA-Seq (Cuffquant)data:workflow:rnaseq:featurecounts:qc
- BBDuk - STAR - featureCounts - QC (paired-end), BBDuk - STAR - featureCounts - QC (single-end)data:workflow:rnaseq:htseq
- Cutadapt - STAR - HTSeq-count (paired-end), Cutadapt - STAR - HTSeq-count (single-end), Trimmomatic - HISAT2 - HTSeq-count (paired-end), Trimmomatic - HISAT2 - HTSeq-count (single-end)data:workflow:rnaseq:htseq:paired
- BBDuk - STAR - HTSeq-count (paired-end)data:workflow:rnaseq:htseq:single
- BBDuk - STAR - HTSeq-count (single-end)data:workflow:rnaseq:rsem
- Cutadapt - STAR - RSEM (Diagenode CATS, paired-end), Cutadapt - STAR - RSEM (Diagenode CATS, single-end)data:workflow:rnaseq:salmon
- BBDuk - Salmon - QC (paired-end), BBDuk - Salmon - QC (single-end)data:workflow:slamdunk
- Slamdunk analysis (paired-end)data:workflow:trimalquant
- shRNA quantificationdata:workflow:wes
- Whole exome sequencing (WES) analysisdata:workflow:wgbs
- WGBS