Commit 1b0e7cce authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

update

parent a03625f7
......@@ -21,33 +21,32 @@ doc: |
- kallisto (transcript [pseudo]counts)
outputs:
files_to_folder_fastqc:
filtered_stats:
label: Filtered statistics
doc: Statistics on quality and preprocessing of the reads
type: Directory
label: FASTQC
doc: Quality reporting by FASTQC
outputSource: quality/files_to_folder_fastqc
files_to_folder_filtered:
label: Filtered reads folder
doc: Output folder with filtered reads.
type: Directory
outputSource: quality/files_to_folder_filtered
files_to_folder_bowtie2:
outputSource: workflow_quality/reports_folder
bowtie2_output:
type: Directory
label: bowtie2 output
doc: bowtie2 mapping results folder. Contains sorted bam file, metrics file and mapping statistics (stdout).
outputSource: bowtie2_files_to_folder/results
files_to_folder_featurecounts:
featurecounts_output:
type: Directory
label: FeatureCounts output
doc: FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout).
outputSource: featurecounts_files_to_folder/results
files_to_folder_kallisto:
kallisto_output:
type: Directory
label: kallisto output
doc: kallisto results folder. Contains transcript abundances, run info and summary.
outputSource: kallisto_files_to_folder/results
inputs:
identifier:
type: string
doc: Identifier for this dataset used in this workflow
label: identifier used
threads:
type: int?
doc: number of threads to use for computational processes
......@@ -60,20 +59,15 @@ inputs:
default: 4000
filter_rrna:
type: boolean
label: Filer rRNA
label: Filter rRNA
doc: Filter rRNA from reads if true
default: false
prefix_id:
type: string
label: Filename prefix
doc: Prefix of the output filenames.
default: out
forward_reads:
type: File
type: string[]
doc: forward sequence file locally
label: forward reads
reverse_reads:
type: File
type: string[]
doc: reverse sequence file locally
label: reverse reads
bowtie2-indexfolder:
......@@ -89,6 +83,11 @@ inputs:
label: GTF file
doc: GTF file location
contamination_references:
type: string[]
doc: bbmap reference fasta file for contamination filtering
label: contamination reference file
destination:
type: string?
label: Output Destination
......@@ -96,31 +95,34 @@ inputs:
steps:
#########################################
# Workflow for quality and filtering using fastqc, fastp and optionally bbduk
quality:
# Workflow for quality and filtering of raw reads
workflow_quality:
label: Quality and filtering workflow
doc: Quality assessment of illumina reads with rRNA filtering option
run: workflow_illumina_quality.cwl
in:
filter_rrna: filter_rrna
prefix_id: prefix_id
forward_reads: forward_reads
reverse_reads: reverse_reads
threads: threads
filter_references: contamination_references
memory: memory
run: workflow_illumina_quality.cwl
out: [files_to_folder_fastqc, files_to_folder_filtered, QC_forward_reads, QC_reverse_reads]
threads: threads
identifier: identifier
filter_rrna: filter_rrna
step:
default: 1
out: [QC_reverse_reads, QC_forward_reads, reports_folder]
#########################################
# bowtie2 alignment
bowtie2:
label: bowtie2
doc: runs bowtie2 alignment on the genome with the quality filtered reads.
run: ../bowtie2/bowtie2_align_simple.cwl
in:
prefix: prefix_id
forward_reads: quality/QC_forward_reads
reverse_reads: quality/QC_reverse_reads
prefix: identifier
forward_reads: workflow_quality/QC_forward_reads
reverse_reads: workflow_quality/QC_reverse_reads
indexfolder: bowtie2-indexfolder
threads: threads
run: ../bowtie2/bowtie2_align_simple.cwl
out:
[sam, metricsfile,bowtie2_stats]
#########################################
......@@ -128,13 +130,13 @@ steps:
sam_to_sorted-bam:
label: sam to sorted bam
doc: Converts a SAM file to a sorted BAM file
run: ../samtools/sam_to_sorted-bam.cwl
in:
prefix:
source: prefix_id
identifier:
source: identifier
valueFrom: $(self+"_bowtie2")
sam: bowtie2/sam
threads: threads
run: ../samtools/sam_to_sorted-bam.cwl
out:
[sortedbam]
#########################################
......@@ -142,13 +144,13 @@ steps:
featurecounts:
label: FeatureCounts
doc: Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts.
run: ../RNAseq/featurecounts.cwl
in:
prefix: prefix_id
prefix: identifier
bam: sam_to_sorted-bam/sortedbam
gtf: gtf
threads: threads
when: $(inputs.gtf != undefined)
run: ../RNAseq/featurecounts.cwl
out:
[readcounts, summary, overview]
#########################################
......@@ -156,15 +158,15 @@ steps:
kallisto:
label: kallisto
doc: Calculates transcript abundances
run: ../RNAseq/kallisto/kallisto_quant.cwl
in:
gtf: gtf
prefix: prefix_id
forward_reads: quality/QC_forward_reads
reverse_reads: quality/QC_reverse_reads
prefix: identifier
forward_reads: workflow_quality/QC_forward_reads
reverse_reads: workflow_quality/QC_reverse_reads
indexfolder: kallisto-indexfolder
threads: threads
when: $(inputs.gtf != undefined)
run: ../RNAseq/kallisto/kallisto_quant.cwl
out:
[abundance.h5, abundance.tsv, run_info, summary]
......@@ -173,6 +175,7 @@ steps:
bowtie2_files_to_folder:
label: bowtie2 output
doc: Preparation of bowtie2 output files to a specific output folder
run: ../expressions/files_to_folder.cwl
in:
files:
source: [sam_to_sorted-bam/sortedbam, bowtie2/metricsfile, bowtie2/bowtie2_stats]
......@@ -180,13 +183,13 @@ steps:
pickValue: all_non_null
destination:
default: "3_bowtie2-alignment"
run: ../expressions/files_to_folder.cwl
out:
[results]
featurecounts_files_to_folder:
label: FeatureCounts output
doc: Preparation of FeatureCounts output files to a specific output folder
run: ../expressions/files_to_folder.cwl
in:
gtf: gtf
files:
......@@ -196,13 +199,13 @@ steps:
destination:
default: "4_FeatureCounts"
when: $(inputs.gtf != undefined)
run: ../expressions/files_to_folder.cwl
out:
[results]
kallisto_files_to_folder:
label: kallisto output
doc: Preparation of kallisto output files to a specific output folder
run: ../expressions/files_to_folder.cwl
in:
gtf: gtf
files:
......@@ -212,7 +215,6 @@ steps:
destination:
default: "5_Kallisto"
when: $(inputs.gtf != undefined)
run: ../expressions/files_to_folder.cwl
out:
[results]
#############################################
......
......@@ -20,33 +20,32 @@ doc: |
- kallisto (transcript [pseudo]counts)
outputs:
files_to_folder_fastqc:
filtered_stats:
label: Filtered statistics
doc: Statistics on quality and preprocessing of the reads
type: Directory
label: FASTQC
doc: Quality reporting by FASTQC
outputSource: quality/files_to_folder_fastqc
files_to_folder_filtered:
type: Directory
label: Filtered reads folder
doc: Output folder with filtered reads.
outputSource: quality/files_to_folder_filtered
files_to_folder_STAR:
outputSource: workflow_quality/reports_folder
STAR_output:
type: Directory
label: STAR output folder
doc: STAR results folder. Contains logs, bam file, readcounts per gene and splice_junctions.
outputSource: STAR_files_to_folder/results
files_to_folder_featurecounts:
featurecounts_output:
type: Directory
label: FeatureCounts output
doc: FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout).
outputSource: featurecounts_files_to_folder/results
files_to_folder_kallisto:
kallisto_output:
type: Directory
label: kallisto output
doc: kallisto results folder. Contains transcript abundances, run info and summary.
outputSource: kallisto_files_to_folder/results
inputs:
identifier:
type: string
doc: Identifier for this dataset used in this workflow
label: identifier used
threads:
type: int?
doc: number of threads to use for computational processes
......@@ -60,16 +59,12 @@ inputs:
filter_rrna:
type: boolean
default: true
prefix_id:
type: string
doc: prefix of the filename outputs
default: out
forward_reads:
type: File
type: string[]
doc: forward sequence file locally
label: forward reads
reverse_reads:
type: File
type: string[]
doc: reverse sequence file locally
label: reverse reads
......@@ -94,6 +89,11 @@ inputs:
- GeneCounts
doc: Run with get gene quantification
contamination_references:
type: string[]
doc: bbmap reference fasta file for contamination filtering
label: contamination reference file
destination:
type: string?
label: Output Destination
......@@ -101,30 +101,33 @@ inputs:
steps:
#########################################
# Workflow for quality and filtering using fastqc, fastp and optionally bbduk
quality:
# Workflow for quality and filtering of raw reads
workflow_quality:
label: Quality and filtering workflow
doc: Quality assessment of illumina reads with rRNA filtering option
run: workflow_illumina_quality.cwl
in:
filter_rrna: filter_rrna
prefix_id: prefix_id
forward_reads: forward_reads
reverse_reads: reverse_reads
threads: threads
filter_references: contamination_references
memory: memory
run: workflow_illumina_quality.cwl
out: [files_to_folder_fastqc, files_to_folder_filtered, QC_forward_reads, QC_reverse_reads]
threads: threads
identifier: identifier
filter_rrna: filter_rrna
step:
default: 1
out: [QC_reverse_reads, QC_forward_reads, reports_folder]
#########################################
# STAR alignment
STAR:
label: STAR
doc: runs STAR alignment on the genome with the quality filtered reads.
in:
forward_reads: quality/QC_forward_reads
reverse_reads: quality/QC_reverse_reads
forward_reads: workflow_quality/QC_forward_reads
reverse_reads: workflow_quality/QC_reverse_reads
OutFileNamePrefix:
source: prefix_id
source: identifier
valueFrom: $(self+"_")
genomeDir: STAR-indexfolder
sjdbGTFfile: gtf
......@@ -141,7 +144,7 @@ steps:
label: FeatureCounts
doc: Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts.
in:
prefix: prefix_id
prefix: identifier
bam: STAR/bam
gtf: gtf
threads: threads
......@@ -154,9 +157,9 @@ steps:
label: kallisto
doc: Calculates transcript abundances
in:
prefix: prefix_id
forward_reads: quality/QC_forward_reads
reverse_reads: quality/QC_reverse_reads
prefix: identifier
forward_reads: workflow_quality/QC_forward_reads
reverse_reads: workflow_quality/QC_reverse_reads
indexfolder: kallisto-indexfolder
threads: threads
run: ../RNAseq/kallisto/kallisto_quant.cwl
......@@ -169,7 +172,7 @@ steps:
label: STAR output
doc: Preparation of STAR output files to a specific output folder
in:
files:
files:
source: [STAR/bam, STAR/log_file, STAR/final_log_file, STAR/reads_per_gene, STAR/splice_junctions]
linkMerge: merge_flattened
pickValue: all_non_null
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment