Commit 071ab123 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

labels,docs and naming

parent e1fe8b82
......@@ -7,29 +7,33 @@ requirements:
MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
label: Read quality control, trimming and contamination filter.
label: Illumina read quality control, trimming and contamination filter.
doc: |
Workflow for (paired) read quality control, trimming and contamination filtering.
Will output a merged set of read pairs, when multiple datasets are used.
Workflow for Illumina paired read quality control, trimming and filtering.
Multiple read pairs will be merged into single paired dataset.
Steps:
- FastQC (read quality control)
- FastQC (on raw data files)
- fastp (read quality trimming)
- Kraken2 taxonomic classification of reads
- bbduk used for phix and/or rrna filtering
- bbmap for (contamination) filtering
- FastQC (on filtered (merged) data)
outputs:
reports_to_folder:
reports_folder:
type: Directory
label: Filtering reports folder
doc: Folder containing all reports of filtering and quality control
outputSource: reports_files_to_folder/results
QC_forward_reads:
type: File
label: Filtered forward read
doc: Filtered forward read
outputSource: phix_filter/out_forward_reads
QC_reverse_reads:
type: File
label: Filtered reverse read
doc: Filtered reverse read
outputSource: phix_filter/out_reverse_reads
inputs:
......@@ -74,7 +78,7 @@ inputs:
default: false
run_kraken2:
type: boolean?
doc: Optionally run Kraken2 contamination inspection
doc: Optionally run Kraken2
label: Kraken2
default: true
kraken_database:
......@@ -112,9 +116,10 @@ steps:
#############################################
#### merging of FASTQ files to only one
fastq_merge_fwd:
run: ../bash/concatenate.cwl
fastq_merge_fwd:
label: Merge forward reads
doc: Merge multiple forward fastq reads to a single file
run: ../bash/concatenate.cwl
in:
identifier: identifier
# infiles:
......@@ -131,6 +136,7 @@ steps:
fastq_merge_rev:
label: Merge reverse reads
doc: Merge multiple reverse fastq reads to a single file
run: ../bash/concatenate.cwl
in:
identifier: identifier
......@@ -189,6 +195,7 @@ steps:
#### Merging of reference files
combine_references:
label: Combine references
doc: Combine references to a single fasta file
run: ../bash/concatenate.cwl
in:
# infiles:
......
......@@ -27,7 +27,7 @@ outputs:
label: Filtered statistics
doc: Statistics on quality and preprocessing of the reads
type: Directory
outputSource: workflow_quality/reports_to_folder
outputSource: workflow_quality/reports_folder
kraken2_output:
label: Kraken2 reports
doc: Kraken2 taxonomic classification reports
......@@ -137,7 +137,7 @@ steps:
identifier: identifier
step:
default: 1
out: [QC_reverse_reads, QC_forward_reads, reports_to_folder]
out: [QC_reverse_reads, QC_forward_reads, reports_folder]
#############################################
#### Kraken2
......@@ -148,7 +148,7 @@ steps:
in:
tmp_id: identifier
identifier:
valueFrom: $(inputs.tmp_id)_filtered_illumina
valueFrom: $(inputs.tmp_id)_illumina_filtered
threads: threads
database: kraken_database
forward_reads: workflow_quality/QC_forward_reads
......
......@@ -300,7 +300,7 @@ steps:
### Move to folder if not part of a workflow
busco_files_to_folder:
doc: Preparation of BUSCO output files to a specific output folder
label: BUSCO output
label: BUSCO output folder
run: ../expressions/files_to_folder.cwl
in:
files:
......
......@@ -31,12 +31,12 @@ outputs:
label: Read quality and filtering reports
doc: Quality reports
type: Directory
outputSource: workflow_quality_nanopore/reports_to_folder
outputSource: workflow_quality_nanopore/reports_folder
illumina_quality_stats:
label: Filtered statistics
doc: Statistics on quality and preprocessing of the reads
type: Directory
outputSource: workflow_quality_illumina/reports_to_folder
outputSource: workflow_quality_illumina/reports_folder
kraken2_output:
label: Kraken2 reports
doc: Kraken2 taxonomic classification reports
......@@ -149,7 +149,7 @@ steps:
identifier: identifier
step:
default: 1
out: [filtered_reads, reports_to_folder]
out: [filtered_reads, reports_folder]
#############################################
#### Quality Illumina
workflow_quality_illumina:
......@@ -169,7 +169,7 @@ steps:
identifier: identifier
step:
default: 2
out: [QC_reverse_reads, QC_forward_reads, reports_to_folder]
out: [QC_reverse_reads, QC_forward_reads, reports_folder]
#############################################
#### Taxonomic classification of with Kraken2
nanopore_kraken2:
......
......@@ -17,15 +17,15 @@ doc: |
- FastQC after filtering (read quality control)
outputs:
reports_to_folder:
reports_folder:
type: Directory
label: Filtered reads folder
doc: Output folder with filtered reads, stats and reports.
label: Filtering reports folder
doc: Folder containing all reports of filtering and quality control
outputSource: reports_files_to_folder/results
filtered_reads:
type: File
label: Filtered reads
doc: Contamination filtered reads
label: Filtered nanopore reads
doc: Filtered nanopore reads
outputSource: reference_filter_nanopore/fastq
inputs:
......@@ -89,7 +89,7 @@ steps:
# source: [nanopore_fastq_reads]
# linkMerge: merge_flattened
# pickValue: all_non_null
file_paths:
file_paths:
source: reads
linkMerge: merge_flattened
pickValue: all_non_null
......
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