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 aggregator

• data:alignment - Abstract alignment process

• data:alignment:bam:bamclipped: - Bamclipper

• data:alignment:bam:bowtie1 - Bowtie (Dicty)

• data:alignment:bam:bowtie2 - Bowtie2

• data:alignment:bam:bqsr: - BaseQualityScoreRecalibrator

• data:alignment:bam:bwaaln - BWA ALN

• data:alignment:bam:bwamem - BWA MEM

• data:alignment:bam:bwamem2 - BWA MEM2

• data:alignment:bam:bwasw - BWA SW

• data:alignment:bam:hisat2 - HISAT2

• data:alignment:bam:markduplicate: - MarkDuplicates

• data:alignment:bam:primary - Bam split

• data:alignment:bam:rnaseqvc: - RNA-seq variant calling preprocess

• data:alignment:bam:samtools: - Samtools view

• data:alignment:bam:scseq: - Single cell BAM file and index

• data:alignment:bam:secondary - Secondary hybrid BAM file

• data:alignment:bam:sieve: - alignmentSieve

• data:alignment:bam:splitncigar: - GATK SplitNCigarReads

• data:alignment:bam:star: - STAR

• data:alignment:bam:umitools:dedup: - UMI-tools dedup

• data:alignment:bam:upload - BAM file, BAM file and index

• data:alignment:bam:walt - WALT

• data:alignment:bam:wgsbwa2: - WGS preprocess data with bwa-mem2

• data:annotation - Abstract annotation process

• data:annotation:cuffmerge - Cuffmerge

• data:annotation:gff3 - GFF3 file

• data:annotation:gtf - Convert GFF3 to GTF, GTF file

• data:archive:samples - Archive samples

• data:bam:plot:bamliquidator - Bamliquidator

• data:bam:plot:bamplot - Bamplot

• data:bed - Abstract bed process, BED file

• data:bedcov: - Samtools bedcov

• data:bedpe: - BEDPE file, Bedtools bamtobed

• data:chipqc: - ChipQC

• data:chipseq:batch:macs2 - ChIP-seq (MACS2), ChIP-seq (MACS2-ROSE2)

• data:chipseq:callpeak:macs14 - MACS 1.4

• data:chipseq:callpeak:macs2: - MACS 2.0

• data:chipseq:genescore - ChIP-Seq (Gene Score)

• data:chipseq:peakscore - ChIP-Seq (Peak Score)

• data:chipseq:rose2: - ROSE2

• data:clustering:hierarchical:etc: - Hierarchical clustering of time courses

• data:coverage:bigwig: - Calculate coverage (bamCoverage)

• data:cufflinks:cufflinks - Cufflinks 2.2

• data:cufflinks:cuffquant - Cuffquant 2.2, Cuffquant results

• data:cuffnorm - Cuffnorm

• data:differentialexpression - Abstract differential expression process

• data:differentialexpression:cuffdiff: - Cuffdiff 2.2

• data:differentialexpression:deseq2: - DESeq2

• data:differentialexpression:edger: - edgeR

• data:differentialexpression:upload - Differential Expression (table)

• data:etc - Expression Time Course, Expression time course

• data:expression - Abstract expression process

• data:expression:polya - Dictyostelium expressions

• data:expression:shrna2quant - Quantify shRNA species using bowtie2

• data:expressionset - Expression matrix

• data:expressionset:etc - Merge Expressions (ETC)

• data:file: - BaseSpace file

• data:gaf:2:0 - GAF file

• data:geneset: - Gene set, Gene set (create)

• data:geneset:venn: - Gene set (create from Venn diagram)

• data:genomeindex:10x: - Cell Ranger Mkref

• data:genomicsdb: - GATK GenomicsDBImport

• data:geo: - GEO import

• data:index:bowtie2: - Bowtie2 genome index

• data:index:bowtie: - Bowtie genome index

• data:index:bwa: - BWA genome index

• data:index:bwamem2: - BWA-MEM2 genome index, BWA-MEM2 index files

• data:index:hisat2: - HISAT2 genome index

• data:index:salmon - Salmon Index

• data:index:star: - STAR genome index

• data:index:walt: - WALT genome index

• data:junctions:regtools - Annotate novel splice junctions (regtools)

• data:mappability:bcm - Mappability, Mappability info

• data:mergereads:paired: - Merge FASTQ (paired-end)

• data:mergereads:single: - Merge FASTQ (single-end)

• data:metadata: - Metadata table

• data:metadata:unique: - Metadata table (one-to-one)

• data:methylationarray:idat: - IDAT file

• data:microarray:mapping: - Map microarray probes

• data:microarray:normalized: - Upload microarray expression (unmapped)

• data:ml:table:expressions: - ML-ready expression

• data:multiplexed:qseq:paired - Reads (QSEQ multiplexed, paired)

• data:multiplexed:qseq:single - Reads (QSEQ multiplexed, single)

• data:multiqc: - MultiQC

• data:ontology:obo - OBO file

• data:other:geo:chipseq - Prepare GEO - ChIP-Seq

• data:other:geo:rnaseq - Prepare GEO - RNA-Seq

• data:pca - PCA

• data:picard:insert: - Picard InsertSizeMetrics

• data:picard:rrbs: - Picard CollectRrbsMetrics

• data:picard:summary: - Picard AlignmentSummary

• data:picard:wgsmetrics: - Picard WGS Metrics

• data:prepeakqc - Pre-peakcall QC

• data:proteomics:massspectrometry: - Upload proteomics sample

• data:proteomics:sampleset: - Upload proteomics sample set

• data:qorts:qc: - QoRTs QC

• data:reads:fastq:paired: - Convert files to reads (paired-end), FASTQ file (paired-end), SRA data (paired-end)

• data:reads:fastq:paired:bamtofastq: - Samtools fastq (paired-end)

• data:reads:fastq:paired:bbduk: - BBDuk (paired-end)

• data:reads:fastq:paired:cutadapt - Cutadapt (paired-end)

• data:reads:fastq:paired:cutadapt: - Cutadapt (Corall RNA-Seq, paired-end)

• data:reads:fastq:paired:seqtk: - Reverse complement FASTQ (paired-end), Subsample FASTQ (paired-end)

• data:reads:fastq:paired:trimgalore: - Trim Galore (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 (single-end)

• data:reads:fastq:single:cutadapt: - Cutadapt (3’ mRNA-seq, single-end), Cutadapt (Corall RNA-Seq, single-end)

• data:reads:fastq:single:seqtk: - Reverse complement FASTQ (single-end), Subsample FASTQ (single-end)

• data:reads:fastq:single:trimmomatic - Trimmomatic (single-end)

• data:rnaseqc:qc: - RNA-SeQC

• data:sam:header - SAM header

• data:samtools:idxstats: - Samtools idxstats

• data:samtoolscoverage:multi: - Samtools coverage (multi-sample)

• data:samtoolscoverage:single: - Samtools coverage (single-sample)

• data:scexpression:10x: - Cell Ranger Count

• data:screads:10x: - Reads (scRNA 10x)

• data:seq:nucleotide: - FASTA file

• data:shrna:differentialexpression: - Differential expression of shRNA

• data:similarexpression: - Find similar genes

• data:spikeins - Spike-ins quality control

• data:sra: - SRA data

• data:strandedness - Detect library strandedness

• data:test:disabled - Test disabled inputs

• data:test:fields - Test basic fields

• data:test:hidden - Test hidden inputs

• data:test:result - Test select controler, Test sleep progress

• data:variants:gvcf: - GATK HaplotypeCaller (GVCF)

• data:variants:vcf - VCF file

• data:variants:vcf:chemut: - Variant calling (CheMut)

• data:variants:vcf:filtering: - Variant filtering (CheMut)

• data:variants:vcf:gatk:hc: - GATK4 (HaplotypeCaller)

• data:variants:vcf:genotypegvcfs: - GATK GenotypeGVCFs

• data:variants:vcf:mergevcfs: - GATK MergeVcfs

• data:variants:vcf:refinevariants: - GATK refine variants

• data:variants:vcf:selectvariants: - GATK SelectVariants (multi-sample)

• data:variants:vcf:selectvariants:single: - GATK SelectVariants (single-sample)

• data:variants:vcf:snpeff: - snpEff (General variant annotation) (multi-sample)

• data:variants:vcf:snpeff:single: - snpEff (General variant annotation) (single-sample)

• data:variants:vcf:variantfiltration: - GATK VariantFiltration (multi-sample)

• data:variants:vcf:variantfiltration:single: - GATK VariantFiltration (single-sample)

• data:variants:vcf:vep: - Ensembl Variant Effect Predictor

• data:variants:vcf:vqsr: - GATK filter variants (VQSR)

• data:variantstable: - GATK VariantsToTable

• data:vep:cache: - Ensembl-VEP cache directory

• data:wgbs:bsrate: - Bisulfite conversion rate

• data:wgbs:hmr - HMR

• data:wgbs:methcounts - methcounts

• data:workflow:atacseq - ATAC-Seq

• data:workflow:chemut - Chemical Mutagenesis

• data:workflow:chipseq:macs2rose2 - MACS2, MACS2 - ROSE2

• data:workflow:chipseq:seqtkbwaaln - Subsample FASTQ and BWA Aln (paired-end), Subsample FASTQ and BWA Aln (single-end)

• data:workflow:cutnrun - Cut & Run

• data:workflow:cutnrun: - Beta Cut & Run workflow

• data:workflow:mirna - miRNA pipeline

• data:workflow:quant:featurecounts: - QuantSeq workflow

• 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

• data:workflow:rnaseq:salmon: - BBDuk - Salmon - QC

• data:workflow:rnaseq:star:qc: - STAR-based gene quantification workflow

• data:workflow:rnaseq:variants: - RNA-seq Variant Calling Workflow

• data:workflow:trimalquant - shRNA quantification

• data:workflow:wes - Whole exome sequencing (WES) analysis

• data:workflow:wgbs - WGBS (paired-end), WGBS (single-end)

• data:workflow:wgs - WGS (paired-end) analysis

• data:workflow:wgs:gvcf: - WGS analysis (GVCF)

• data:xengsort:classification: - Xengsort classify

• data:xengsort:index: - Xengsort index