Commit 2dd80284 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

accept multiple kraken2 databases and run them seperately

parent ecaf2d09
......@@ -10,13 +10,13 @@ requirements:
label: Illumina read quality control, trimming and contamination filter.
doc: |
**Workflow for Illumina paired read quality control, trimming and filtering.**<br />
Multiple read pairs will be merged into single paired dataset.<br />
Multiple paired datasets will be merged into single paired dataset.<br />
Summary:
- FastQC on raw data files<br />
- fastp for read quality trimming<br />
- Kraken2 for taxonomic classification of reads<br />
- BBduk for phix and rRNA filtering<br />
- BBmap for (contamination) filtering using given references<br />
- BBduk for phiX and (optional) rRNA filtering<br />
- Kraken2 for taxonomic classification of reads (optional)<br />
- BBmap for (contamination) filtering using given references (optional)<br />
- FastQC on filtered (merged) data<br />
**All tool CWL files and other workflows can be found here:**<br>
......@@ -89,10 +89,10 @@ inputs:
label: Deduplicate reads
default: false
kraken_database:
type: string?
type: string[]?
doc: Kraken2 database location
label: Kraken2 database
default: "/unlock/references/databases/Kraken2/K2_PlusPF_20210517"
default: ["/unlock/references/databases/Kraken2/K2_PlusPF_20210517"]
keep_reference_mapped_reads:
type: boolean
......@@ -185,8 +185,8 @@ steps:
source: identifier
valueFrom: $(self+"_rRNA-filter")
filter_rrna: filter_rrna
forward_reads: reference_filter_illumina/out_forward_reads
reverse_reads: reference_filter_illumina/out_reverse_reads
forward_reads: fastp/out_forward_reads
reverse_reads: fastp/out_reverse_reads
reference:
valueFrom: "/unlock/references/databases/riboKmers.fa.gz"
threads: threads
......@@ -226,10 +226,11 @@ steps:
doc: Taxonomic classification of FASTQ reads
when: $(inputs.kraken_database !== null)
run: ../kraken2/kraken2.cwl
scatter: database
in:
tmp_id: identifier
identifier:
valueFrom: $(inputs.tmp_id)_unfiltered_illumina
valueFrom: $(inputs.tmp_id)_Qfiltered
threads: threads
kraken_database: kraken_database
database: kraken_database
......@@ -244,6 +245,7 @@ steps:
doc: Visualization of Kraken2 classification with Krona
when: $(inputs.kraken_database !== null)
run: ../krona/krona.cwl
scatter: kraken
in:
kraken_database: kraken_database
kraken: illumina_quality_kraken2/sample_report
......
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