Add fq2bam fq align dd bwamem #9309
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| { | ||
| "nextflow.formatting.harshilAlignment": true, | ||
| "nextflow.telemetry.enabled": true | ||
| } | ||
Submodule setup-nextflow
added at
6c2e22
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,3 @@ | ||
| process { | ||
| withName: 'SAMTOOLS_SORT' { | ||
| ext.prefix = { "${meta.id}.sorted" } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,213 @@ | ||
| nextflow_workflow { | ||
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| name "Test Subworkflow FASTQ_ALIGN_DEDUP_BWAMEM" | ||
| script "../main.nf" | ||
| workflow "FASTQ_ALIGN_DEDUP_BWAMEM" | ||
| config "./nextflow.config" | ||
|
|
||
| tag "gpu" | ||
| tag "subworkflows" | ||
| tag "subworkflows_nfcore" | ||
| tag "subworkflows/fastq_align_dedup_bwamem" | ||
| tag "parabricks/fq2bam" | ||
| tag "samtools/index" | ||
| tag "picard/markduplicates" | ||
| tag "bwa" | ||
| tag "bwa/index" | ||
| tag "parabricks/fq2bam" | ||
| tag "samtools" | ||
| tag "samtools/sort" | ||
| tag "samtools/index" | ||
| tag "samtools/idxstats" | ||
| tag "samtools/flagstat" | ||
| tag "samtools/stats" | ||
| tag "bam_sort_stats_samtools" | ||
| tag "picard/markduplicates" | ||
| tag "picard/addorreplacereadgroups" | ||
|
|
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| setup { | ||
| run("BWA_INDEX") { | ||
| script "../../../../modules/nf-core/bwa/index/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
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| test("Sarscov2 fasta - SE - deduplicate - with GPU parabricks/fq2bam") { | ||
| when { | ||
| workflow { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:true ], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) | ||
| ]) | ||
| input[1] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ]) | ||
| input[2] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) | ||
| ]) | ||
| input[3] = BWA_INDEX.out.index | ||
| input[4] = false // skip_deduplication | ||
| input[5] = true // use_gpu | ||
| input[6] = [[:], [] ] // interval_file | ||
| input[7] = [[:], [] ] // known_sites | ||
| input[8] = "bam" // output_fmt | ||
|
Comment on lines
55
to
60
Contributor
There was a problem hiding this comment. Your variables are not passed correcty, ch_reads // channel: [ val(meta), [ reads ] ] Outfmt comes before interval_file & known sites
Contributor
Author
There was a problem hiding this comment. thanks, that totally went under my radar!
Contributor
Author
There was a problem hiding this comment. fixed, still get error: |
||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot( | ||
| workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, | ||
| workflow.out.bai.collect { meta, bai -> file(bai).name }, | ||
| workflow.out.samtools_flagstat, | ||
| workflow.out.samtools_stats, | ||
| workflow.out.samtools_index_stats, | ||
| workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, | ||
| workflow.out.multiqc.flatten().collect { path -> file(path).name }, | ||
| workflow.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("Sarscov2 fasta - SE - skip deduplication - with GPU parabricks/fq2bam") { | ||
| when { | ||
| workflow { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:true ], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) | ||
| ]) | ||
| input[1] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ]) | ||
| input[2] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) | ||
| ]) | ||
| input[3] = BWA_INDEX.out.index | ||
| input[4] = true // skip_deduplication | ||
| input[5] = true // use_gpu | ||
| input[6] = Channel.of([[:], []]) // interval_file | ||
| input[7] = Channel.of([[:], []]) // known_sites | ||
| input[8] = "bam" // output_fmt | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot( | ||
| workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, | ||
| workflow.out.bai.collect { meta, bai -> file(bai).name }, | ||
| workflow.out.samtools_flagstat, | ||
| workflow.out.samtools_stats, | ||
| workflow.out.samtools_index_stats, | ||
| workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, | ||
| workflow.out.multiqc.flatten().collect { path -> file(path).name }, | ||
| workflow.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
|
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| test("Sarscov2 fasta - PE - skip deduplication - with GPU parabricks/fq2bam") { | ||
|
|
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| when { | ||
| workflow { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) | ||
| ] | ||
| ]) | ||
| input[1] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ]) | ||
| input[2] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) | ||
| ]) | ||
| input[3] = BWA_INDEX.out.index | ||
| input[4] = true // skip_deduplication | ||
| input[5] = true // use_gpu | ||
| input[6] = Channel.of([[:], []]) // interval_file | ||
| input[7] = Channel.of([[:], []]) // known_sites | ||
| input[8] = "bam" // output_fmt | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot( | ||
| workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, | ||
| workflow.out.bai.collect { meta, bai -> file(bai).name }, | ||
| workflow.out.samtools_flagstat, | ||
| workflow.out.samtools_stats, | ||
| workflow.out.samtools_index_stats, | ||
| workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, | ||
| workflow.out.multiqc.flatten().collect { path -> file(path).name }, | ||
| workflow.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
|
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| test("Sarscov2 fasta - SE - skip deduplication - with GPU parabricks/fq2bam - stub") { | ||
| options '-stub' | ||
| when { | ||
| workflow { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:true ], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) | ||
| ]) | ||
| input[1] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ]) | ||
| input[2] = Channel.of([ | ||
| [:], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) | ||
| ]) | ||
| input[3] = BWA_INDEX.out.index | ||
| input[4] = false // deduplicate | ||
| input[5] = true // use_gpu | ||
| input[6] = Channel.of([[:], []]) // interval_file | ||
| input[7] = Channel.of([[:], []]) // known_sites | ||
| input[8] = "bam" // output_fmt | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot( | ||
| workflow.out, | ||
| workflow.out.versions.collect{ path(it).yaml } | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
| } | ||
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