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: ...@@ -185,10 +185,10 @@ steps:
out: [standard_report, sample_report] out: [standard_report, sample_report]
illumina_kraken2: illumina_kraken2:
label: Kraken2 workflow label: Taxonomic classification with Kraken2
doc: Read taxonomic classification using the Kraken2 doc: Taxonomic classification of FASTQ reads
when: $(inputs.binning) when: $(inputs.binning)
run: ../metagenomics/kraken2/kraken2.cwl run: ../kraken2/kraken2.cwl
in: in:
binning: binning binning: binning
tmp_id: identifier tmp_id: identifier
...@@ -198,26 +198,29 @@ steps: ...@@ -198,26 +198,29 @@ steps:
database: kraken_database database: kraken_database
forward_reads: workflow_quality_illumina/QC_forward_reads forward_reads: workflow_quality_illumina/QC_forward_reads
reverse_reads: workflow_quality_illumina/QC_forward_reads reverse_reads: workflow_quality_illumina/QC_forward_reads
out: [report, kraken] paired_end:
############################################# default: true
#### Gzip compression of kraken2 files out: [standard_report, sample_report]
kraken2_compress: kraken2_compress:
run: ../bash/pigz.cwl run: ../bash/pigz.cwl
label: Compress kraken2
doc: Compress large kraken2 report file
scatter: inputfile scatter: inputfile
in: in:
inputfile: [nanopore_kraken2/standard_report, illumina_kraken2/kraken] inputfile: [nanopore_kraken2/standard_report, illumina_kraken2/standard_report]
threads: threads threads: threads
out: [outfile] out: [outfile]
#############################################
#### Visual representation of taxonomic classification
kraken2_krona: kraken2_krona:
label: taxonomic classification visualization label: Krona Kraken2
doc: visualization of taxonomic classification with Krona doc: Visualization of kraken2 with Krona
run: ../krona/krona.cwl run: ../krona/krona.cwl
scatter: kraken scatter: kraken
in: in:
kraken: [nanopore_kraken2/sample_report, illumina_kraken2/report] kraken: [nanopore_kraken2/sample_report, illumina_kraken2/sample_report]
out: [krona_html] out: [krona_html]
############################################# #############################################
#### De novo assembly with Flye #### De novo assembly with Flye
flye: flye:
...@@ -255,7 +258,7 @@ steps: ...@@ -255,7 +258,7 @@ steps:
#### Workflow Pilon assembly polishing #### Workflow Pilon assembly polishing
workflow_pilon: workflow_pilon:
label: Pilon label: Pilon
doc: Short reads assembly polishing with Pilon doc: Illumina reads assembly polishing with Pilon
when: $(inputs.binning) when: $(inputs.binning)
run: workflow_pilon_mapping.cwl run: workflow_pilon_mapping.cwl
in: in:
...@@ -273,7 +276,7 @@ steps: ...@@ -273,7 +276,7 @@ steps:
#### Assembly evaluation with QUAST #### Assembly evaluation with QUAST
metaquast_nanopore_pilon: metaquast_nanopore_pilon:
label: Illumina assembly evaluation label: Illumina assembly evaluation
doc: Illumina evaluation of polished assembly with metaQUAST doc: Illumina evaluation of pilon polished assembly with metaQUAST
when: $(inputs.binning) when: $(inputs.binning)
run: ../metaquast/metaquast.cwl run: ../metaquast/metaquast.cwl
in: in:
...@@ -284,8 +287,8 @@ steps: ...@@ -284,8 +287,8 @@ steps:
############################################# #############################################
#### BBmap read mapping (illumina reads) for binning #### BBmap read mapping (illumina reads) for binning
illumina_pilon_readmapping: illumina_pilon_readmapping:
label: BBmap read mapping label: Read mapping
doc: Illumina read mapping using BBmap on assembled contigs doc: Illumina read mapping on pilon assembly for binning
when: $(inputs.binning) when: $(inputs.binning)
run: ../bbmap/bbmap.cwl run: ../bbmap/bbmap.cwl
in: in:
...@@ -326,7 +329,7 @@ steps: ...@@ -326,7 +329,7 @@ steps:
threads: threads threads: threads
step: step:
default: 1 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 #### Move to folder if not part of a workflow
...@@ -336,7 +339,7 @@ steps: ...@@ -336,7 +339,7 @@ steps:
run: ../expressions/files_to_folder.cwl run: ../expressions/files_to_folder.cwl
in: in:
files: 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 linkMerge: merge_flattened
destination: destination:
valueFrom: $("2_Kraken2_classification") valueFrom: $("2_Kraken2_classification")
...@@ -470,7 +473,7 @@ steps: ...@@ -470,7 +473,7 @@ steps:
in: in:
binning: binning binning: binning
folders: 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 linkMerge: merge_flattened
pickValue: all_non_null pickValue: all_non_null
destination: destination:
......
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