Commit e8158958 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

add kraken2+krona and busco fix

parent ab1ac24b
......@@ -28,6 +28,11 @@ outputs:
doc: Statistics on quality and preprocessing of the reads
type: Directory
outputSource: workflow_quality/reports_to_folder
kraken2_output:
label: Kraken2 reports
doc: Kraken2 taxonomic classification reports
type: Directory
outputSource: kraken2_files_to_folder/results
spades_output:
label: SPAdes
doc: Metagenome assembly output by SPADES
......@@ -62,26 +67,6 @@ inputs:
type: string[]
doc: reverse sequence file path
label: reverse reads
use_reference_mapped_reads:
type: boolean
doc: Continue with reads mapped to the given reference
label: Keep mapped reads
default: false
deduplicate:
type: boolean?
doc: Remove exact duplicate reads with fastp
label: Deduplicate reads
default: false
threads:
type: int?
doc: number of threads to use for computational processes
label: number of threads
default: 2
memory:
type: int?
doc: maximum memory usage in megabytes
label: memory usage (MB)
default: 4000
pacbio_reads:
type: File[]?
doc: file with PacBio reads locally
......@@ -94,6 +79,22 @@ inputs:
type: string[]
doc: bbmap reference fasta file paths for contamination filtering
label: contamination reference file
use_reference_mapped_reads:
type: boolean
doc: Continue with reads mapped to the given reference
label: Keep mapped reads
default: false
deduplicate:
type: boolean?
doc: Remove exact duplicate reads with fastp
label: Deduplicate reads
default: false
kraken_database:
type: string
doc: Absolute path with database location of kraken2
label: Kraken2 database
default: "/unlock/references/databases/Kraken2/K2_PlusPF_20210517"
binning:
type: boolean?
label: Run binning workflow
......@@ -106,6 +107,17 @@ inputs:
doc: Run GTDB-Tk taxonomic bin classification when true
default: false
threads:
type: int?
doc: number of threads to use for computational processes
label: number of threads
default: 2
memory:
type: int?
doc: maximum memory usage in megabytes
label: memory usage (MB)
default: 4000
steps:
#############################################
......@@ -126,6 +138,40 @@ steps:
step:
default: 1
out: [QC_reverse_reads, QC_forward_reads, reports_to_folder]
#############################################
#### Kraken2
kraken2:
label: Taxonomic classification with Kraken2
doc: Taxonomic classification of unfiltered FASTQ reads
run: ../kraken2/kraken2.cwl
in:
tmp_id: identifier
identifier:
valueFrom: $(inputs.tmp_id)_unfiltered_illumina
threads: threads
database: kraken_database
forward_reads: workflow_quality/QC_forward_reads
reverse_reads: workflow_quality/QC_reverse_reads
paired_end:
default: true
out: [standard_report, sample_report]
kraken2_compress:
run: ../bash/pigz.cwl
in:
inputfile: kraken2/standard_report
threads: threads
out: [outfile]
kraken2_krona:
label: taxonomic classification visualization
doc: visualization of taxonomic classification with Krona
run: ../krona/krona.cwl
in:
kraken: kraken2/sample_report
out: [krona_html]
#############################################
#### Assembly using SPADES
spades:
......@@ -222,8 +268,22 @@ steps:
run_gtdbtk: run_gtdbtk
step:
default: 1
out: [metabat2_output,checkm_output,gtdbtk_output]
out: [metabat2_output,checkm_output,gtdbtk_output,busco_output]
#############################################
#### Move to folder if not part of a workflow
kraken2_files_to_folder:
doc: Preparation of Kraken2 output files to a specific output folder
label: Kraken2 output folder
run: ../expressions/files_to_folder.cwl
in:
files:
source: [kraken2_compress/outfile, kraken2_krona/krona_html, kraken2/sample_report]
linkMerge: merge_flattened
destination:
valueFrom: $("2_Kraken2_classification")
out:
[results]
#############################################
#### Move to folder if not part of a workflow
spades_files_to_folder:
......@@ -236,7 +296,7 @@ steps:
linkMerge: merge_flattened
pickValue: all_non_null
destination:
valueFrom: $("2_SPAdes_Assembly")
valueFrom: $("3_SPAdes_Assembly")
out:
[results]
#############################################
......@@ -254,7 +314,7 @@ steps:
source: [quast/basicStats, quast/icarusDir]
linkMerge: merge_flattened
destination:
valueFrom: $("3_Quast_AsssemblyQuality_")$(inputs.identifier)
valueFrom: $("4_Quast_AsssemblyQuality_")$(inputs.identifier)
out:
[results]
#############################################
......@@ -268,7 +328,7 @@ steps:
source: [sam_to_sorted_bam/sortedbam, bbmap/stats, contig_read_counts/contigReadCounts, bbmap/covstats, bbmap/log]
linkMerge: merge_flattened
destination:
valueFrom: $("4_BBMAP_ReadMapping")
valueFrom: $("5_BBMAP_ReadMapping")
out:
[results]
#############################################
......@@ -281,11 +341,11 @@ steps:
in:
binning: binning
folders:
source: [workflow_binning/metabat2_output,workflow_binning/checkm_output,workflow_binning/gtdbtk_output]
source: [workflow_binning/metabat2_output,workflow_binning/checkm_output, workflow_binning/gtdbtk_output, workflow_binning/busco_output]
linkMerge: merge_flattened
pickValue: all_non_null
destination:
valueFrom: $("5_Binning")
valueFrom: $("6_Binning")
out:
[results]
#############################################
......
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