Commit 09868055 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

labels and naming

parent 49710b22
......@@ -21,18 +21,15 @@ doc: |
outputs:
reports_to_folder:
type: Directory
label: Filtered reads folder
doc: Output folder with filtered reads, stats and reports.
label: Filtering reports folder
outputSource: reports_files_to_folder/results
QC_forward_reads:
type: File
label: Filtered forward read
doc: Filtered forward read with fastp and (optionally) rrna filtered. (this output is mainly used for other workflows)
outputSource: phix_filter/out_forward_reads
QC_reverse_reads:
type: File
label: Filtered reverse read
doc: Filtered reverse read with fastp and (optionally) rrna filtered. (this output is mainly used for other workflows)
outputSource: phix_filter/out_reverse_reads
inputs:
......@@ -102,7 +99,7 @@ steps:
#############################################
#### FASTQC
fastqc_illumina_before:
label: FastQC
label: FastQC before
doc: Quality assessment and report of reads
run: ../fastqc/fastqc.cwl
in:
......@@ -117,36 +114,36 @@ steps:
#### merging of FASTQ files to only one
fastq_merge_fwd:
run: ../bash/concatenate.cwl
doc: Merge forward reads
label: Merge forward reads
in:
identifier: identifier
# infiles:
# source: [nanopore_fastq_reads]
# linkMerge: merge_flattened
# pickValue: all_non_null
file_paths:
file_paths:
source: forward_reads
linkMerge: merge_flattened
pickValue: all_non_null
outname:
valueFrom: $(inputs.identifier)_merged_1.fq.gz
valueFrom: $(inputs.identifier)_illumina_merged_1.fq.gz
out: [output]
fastq_merge_rev:
fastq_merge_rev:
label: Merge reverse reads
run: ../bash/concatenate.cwl
doc: Merge Reverse reads
in:
identifier: identifier
# infiles:
# source: [nanopore_fastq_reads]
# linkMerge: merge_flattened
# pickValue: all_non_null
file_paths:
file_paths:
source: reverse_reads
linkMerge: merge_flattened
pickValue: all_non_null
outname:
valueFrom: $(inputs.identifier)_merged_2.fq.gz
outname:
valueFrom: $(inputs.identifier)_illumina_merged_2.fq.gz
out: [output]
#############################################
......@@ -165,12 +162,12 @@ steps:
#############################################
#### Kraken2
illumina_quality_kraken2:
label: Taxonomic classification with Kraken2
doc: Taxonomic classification of unfiltered FASTQ reads
label: Kraken2
doc: Taxonomic classification of FASTQ reads
run: ../kraken2/kraken2.cwl
in:
tmp_id: identifier
identifier:
identifier:
valueFrom: $(inputs.tmp_id)_unfiltered_illumina
threads: threads
database: kraken_database
......@@ -181,8 +178,8 @@ steps:
out: [sample_report]
illumina_quality_kraken2_krona:
label: taxonomic classification visualization
doc: visualization of taxonomic classification with Krona
label: Krona
doc: Visualization of Kraken2 classification with Krona
run: ../krona/krona.cwl
in:
kraken: illumina_quality_kraken2/sample_report
......@@ -190,19 +187,20 @@ steps:
#############################################
#### Merging of reference files
merge_references:
combine_references:
label: Combine references
run: ../bash/concatenate.cwl
in:
# infiles:
# source: references
# linkMerge: merge_flattened
# pickValue: all_non_null
file_paths:
file_paths:
source: filter_references
linkMerge: merge_flattened
pickValue: all_non_null
outname:
valueFrom: "merged_references.bbmap.fasta.gz"
valueFrom: "combined_references.fasta.gz"
out: [output]
#########################################
#### Read mapping
......@@ -214,7 +212,7 @@ steps:
identifier: identifier
forward_reads: fastp/out_forward_reads
reverse_reads: fastp/out_reverse_reads
reference: merge_references/output
reference: combine_references/output
output_mapped: keep_reference_mapped_reads
threads: threads
memory: memory
......@@ -247,9 +245,9 @@ steps:
doc: Filters illumina spike-in PhiX sequences from reads using bbduk
run: ../bbmap/bbduk_filter.cwl
in:
identifier:
identifier:
source: identifier
valueFrom: $(self+"_filtered-phix")
valueFrom: $(self+"_illumina_filtered")
forward_reads:
source:
- rrna_filter/out_forward_reads
......@@ -269,7 +267,7 @@ steps:
#############################################
#### FASTQC
fastqc_illumina_after:
label: FastQC
label: FastQC after
doc: Quality assessment and report of reads
run: ../fastqc/fastqc.cwl
in:
......@@ -280,22 +278,17 @@ steps:
#############################################
#### Move to folder if not part of a workflow
reports_files_to_folder:
label: fastp output
label: Reports to folder
doc: Preparation of fastp output files to a specific output folder
run: ../expressions/files_to_folder.cwl
in:
files:
files:
source: [fastqc_illumina_before/html_files, fastqc_illumina_before/zip_files, fastqc_illumina_after/html_files, fastqc_illumina_after/zip_files, fastp/html_report, fastp/json_report, reference_filter_illumina/stats, reference_filter_illumina/covstats, reference_filter_illumina/log, illumina_quality_kraken2/sample_report, illumina_quality_kraken2_krona/krona_html, phix_filter/summary, rrna_filter/summary]
linkMerge: merge_flattened
pickValue: all_non_null
step: step
destination:
destination:
valueFrom: $(inputs.step)_Illumina_Read_Quality
# valueFrom: |
# ${
# var step = inputs.step;
# return step+"_Illumina_Read_Quality";
# }
out:
[results]
......
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