Commit 46089d72 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

label and naming

parent b6186f78
......@@ -81,6 +81,7 @@ steps:
#############################################
#### merging of FASTQ files to only one
merge_nanopore_fastq:
label: Merge fastq files
run: ../bash/concatenate.cwl
in:
identifier: identifier
......@@ -93,12 +94,12 @@ steps:
linkMerge: merge_flattened
pickValue: all_non_null
outname:
valueFrom: $(inputs.identifier)_merged.fastq.gz
valueFrom: $(inputs.identifier)_nanopore_raw.fastq.gz
out: [output]
#############################################
#### FASTQC Before
fastqc_nanopore_before:
label: FastQC
label: FastQC before
doc: Quality assessment and report of reads before filter
in:
nanopore: merge_nanopore_fastq/output
......@@ -107,7 +108,8 @@ steps:
out: [html_files, zip_files]
#############################################
#### merging of contamination reference files
merge_references:
combine_references:
label: Combine references
run: ../bash/concatenate.cwl
in:
# infiles:
......@@ -119,12 +121,12 @@ steps:
linkMerge: merge_flattened
pickValue: all_non_null
outname:
valueFrom: "merged_references.bbmap.fasta.gz"
valueFrom: "combined_references.fasta.gz"
out: [output]
#############################################
#### taxonomic classification of reads with Kraken2
workflow_nanopore_kraken2:
label: Taxonomic classification with Kraken2
label: Kraken2
doc: Taxonomic classification of FASTQ reads
when: $(inputs.run_kraken2)
run: ../kraken2/kraken2.cwl
......@@ -132,7 +134,7 @@ steps:
run_kraken2: run_kraken2
tmp_id: identifier
identifier:
valueFrom: $(inputs.tmp_id)_unfiltered_nanopore
valueFrom: $(inputs.tmp_id)_nanopore_unfiltered_
threads: threads
nanopore: merge_nanopore_fastq/output
database: kraken_database
......@@ -140,7 +142,7 @@ steps:
#############################################
#### Visual representation of taxonomic classification
workflow_krona:
label: taxonomic classification visualization
label: Krona
doc: visualization of taxonomic classification with Krona
run: ../krona/krona.cwl
in:
......@@ -149,13 +151,13 @@ steps:
#############################################
#### Contamination filter
reference_filter_nanopore:
label: Contamination removal
label: Reference mapping
doc: Removal of contaminated reads using minimap2 mapping
run: ../minimap2/minimap2_to_fastq.cwl
in:
threads: threads
identifier: identifier
reference: merge_references/output
reference: combine_references/output
reads: merge_nanopore_fastq/output
output_mapped: keep_reference_mapped_reads
preset:
......@@ -165,7 +167,7 @@ steps:
#############################################
#### FASTQC After
fastqc_nanopore_after:
label: FastQC
label: FastQC after
doc: Quality assessment and report of reads before filter
in:
nanopore: reference_filter_nanopore/fastq
......@@ -176,7 +178,7 @@ 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
in:
files:
......
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