Commit 5a226964 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

change kraken.cwl version and busco fix

parent b6219b59
......@@ -185,10 +185,10 @@ steps:
out: [standard_report, sample_report]
illumina_kraken2:
label: Kraken2 workflow
doc: Read taxonomic classification using the Kraken2
label: Taxonomic classification with Kraken2
doc: Taxonomic classification of FASTQ reads
when: $(inputs.binning)
run: ../metagenomics/kraken2/kraken2.cwl
run: ../kraken2/kraken2.cwl
in:
binning: binning
tmp_id: identifier
......@@ -198,26 +198,29 @@ steps:
database: kraken_database
forward_reads: workflow_quality_illumina/QC_forward_reads
reverse_reads: workflow_quality_illumina/QC_forward_reads
out: [report, kraken]
#############################################
#### Gzip compression of kraken2 files
paired_end:
default: true
out: [standard_report, sample_report]
kraken2_compress:
run: ../bash/pigz.cwl
label: Compress kraken2
doc: Compress large kraken2 report file
scatter: inputfile
in:
inputfile: [nanopore_kraken2/standard_report, illumina_kraken2/kraken]
inputfile: [nanopore_kraken2/standard_report, illumina_kraken2/standard_report]
threads: threads
out: [outfile]
#############################################
#### Visual representation of taxonomic classification
kraken2_krona:
label: taxonomic classification visualization
doc: visualization of taxonomic classification with Krona
label: Krona Kraken2
doc: Visualization of kraken2 with Krona
run: ../krona/krona.cwl
scatter: kraken
in:
kraken: [nanopore_kraken2/sample_report, illumina_kraken2/report]
kraken: [nanopore_kraken2/sample_report, illumina_kraken2/sample_report]
out: [krona_html]
#############################################
#### De novo assembly with Flye
flye:
......@@ -255,7 +258,7 @@ steps:
#### Workflow Pilon assembly polishing
workflow_pilon:
label: Pilon
doc: Short reads assembly polishing with Pilon
doc: Illumina reads assembly polishing with Pilon
when: $(inputs.binning)
run: workflow_pilon_mapping.cwl
in:
......@@ -273,7 +276,7 @@ steps:
#### Assembly evaluation with QUAST
metaquast_nanopore_pilon:
label: Illumina assembly evaluation
doc: Illumina evaluation of polished assembly with metaQUAST
doc: Illumina evaluation of pilon polished assembly with metaQUAST
when: $(inputs.binning)
run: ../metaquast/metaquast.cwl
in:
......@@ -284,8 +287,8 @@ steps:
#############################################
#### BBmap read mapping (illumina reads) for binning
illumina_pilon_readmapping:
label: BBmap read mapping
doc: Illumina read mapping using BBmap on assembled contigs
label: Read mapping
doc: Illumina read mapping on pilon assembly for binning
when: $(inputs.binning)
run: ../bbmap/bbmap.cwl
in:
......@@ -326,7 +329,7 @@ steps:
threads: threads
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
......@@ -336,7 +339,7 @@ steps:
run: ../expressions/files_to_folder.cwl
in:
files:
source: [kraken2_compress/outfile, nanopore_kraken2/sample_report, kraken2_krona/krona_html, illumina_kraken2/report]
source: [kraken2_compress/outfile, kraken2_krona/krona_html, nanopore_kraken2/sample_report, illumina_kraken2/sample_report]
linkMerge: merge_flattened
destination:
valueFrom: $("2_Kraken2_classification")
......@@ -470,7 +473,7 @@ 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:
......
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