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| Original file line number | Diff line number | Diff line change |
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@@ -20,3 +20,5 @@ Makefile | |
| *.bak | ||
| docs/TODO.md | ||
| .git.bak | ||
| assets/schema_input_nfv2.0.0.json | ||
| nextflow_schema_nfv2.json | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,6 +1,6 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| mk-kondo/mikrokondo Nextflow config file | ||
| phac-nml/mikrokondo Nextflow config file | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Default config options for all compute environments | ||
| ---------------------------------------------------------------------------------------- | ||
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@@ -39,10 +39,10 @@ params { | |
| // Sub sampling options | ||
| target_depth = 100 | ||
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| validate_params = false | ||
| validate_params = true | ||
| show_hidden_params = false | ||
| validationS3PathCheck = true | ||
| validationSchemaIgnoreParams = 'output_idx_name,filtered_reads,coverage_calc_fields,assembly_status,coverage_calc_fields.fixed_cov,coverage_calc_fields.auto_cov,assembly_status.report_tag,medaka.model,medaka,validation-S3Path-check,validationS3PathCheck,abricate,python3,pointfinder_db_tag,staramr,mobsuite_recon,skip_staramr,genomes,flye_read_type,shigeifinder,lissero,sistr,ectyper,bandage,bakta,unicycler,medaka,pilon_iterative,pilon,racon,samtools,minimap2,r_contaminants,mash,kraken,checkm,quast_filter,quast,fastqc,spades,flye,chopper,fastp,seqtk,seqtk_size,kat,coreutils,opt_platforms,QCReportFields,QCReport-fields,QCReport,kraken_bin,shigatyper,spatyper,kleborate,subtyping_report,kraken_species,top_hit_species,mash_meta,mlst,raw_reads,abricate_params,target_depth' | ||
| validationSchemaIgnoreParams = 'seqkit,contigs_too_short,output_idx_name,filtered_reads,coverage_calc_fields,assembly_status,coverage_calc_fields.fixed_cov,coverage_calc_fields.auto_cov,assembly_status.report_tag,medaka.model,medaka,validation-S3Path-check,validationS3PathCheck,abricate,python3,pointfinder_db_tag,staramr,mobsuite_recon,skip_staramr,genomes,flye_read_type,shigeifinder,lissero,sistr,ectyper,bandage,bakta,unicycler,medaka,pilon_iterative,pilon,racon,samtools,minimap2,r_contaminants,mash,kraken,checkm,quast_filter,quast,fastqc,spades,flye,chopper,fastp,seqtk,seqtk_size,kat,coreutils,opt_platforms,QCReportFields,QCReport-fields,QCReport,kraken_bin,shigatyper,spatyper,kleborate,subtyping_report,kraken_species,top_hit_species,mash_meta,mlst,raw_reads,abricate_params,target_depth' | ||
| validationFailUnrecognisedParams = false // for the qcreport fields | ||
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| // SKIP options | ||
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@@ -922,8 +922,8 @@ profiles { | |
| } | ||
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| plugins { | ||
| id 'nf-validation' | ||
| // id [email protected] | ||
| //id 'nf-validation@2.0.0' | ||
| id '[email protected]' | ||
| id 'nf-prov' | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,8 +1,8 @@ | ||
| >contig1 | ||
| >contig1 length=1 | ||
| A | ||
| >contig2 | ||
| >contig2 length=2 | ||
| AC | ||
| >contig3 | ||
| >contig3 length=3 | ||
| ACT | ||
| >contig4 | ||
| >contig4 length=4 | ||
| ACTG |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| >contig1 length=10 | ||
| ATCGATCGAT | ||
| >contig2 length=20 | ||
| ATCGATCGATATCGATCGAT | ||
| >contig3 length=30 | ||
| ATCGATCGATATCGATCGATATCGATCGAT |
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| @@ -0,0 +1,2 @@ | ||
| sample,fastq_1,fastq_2,long_reads,assembly | ||
| CSE,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/campy-staph1.fq.gz,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/campy-staph2.fq.gz,, |
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| @@ -0,0 +1,39 @@ | ||
| nextflow_workflow { | ||
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| name "Full Integration Tests for MIKROKONDO" | ||
| script "main.nf" | ||
| workflow "MIKROKONDO" | ||
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| test("Should run without failures") { | ||
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| when { | ||
| params { | ||
| input = "samplesheet-staph.csv" | ||
| platform = "illumina" | ||
| outdir = "results" | ||
| mash.mash_sketch = "campy-staph-ecoli.msh" | ||
| r_contaminants.mega_mm2_idx = "campy.mmi" | ||
| skip_bakta = true | ||
| skip_staramr = true | ||
| skip_mobrecon = true | ||
| skip_checkm = true | ||
| skip_raw_read_metrics = true | ||
| skip_polishing = true | ||
| max_memory = "4.GB" | ||
| max_cpus = 2 | ||
| } | ||
| workflow { | ||
| """ | ||
| // define inputs of the workflow here. Example: | ||
| // input[0] = file("test-file.txt") | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assert workflow.success | ||
| } | ||
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| } | ||
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| } |
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