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* Update stitch * Add bam test and sort snapshot * Set R version for repetability * Add htslib to environment for conda * Fix environment * Add rsync to environment * Fix linting * Update path
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,178 @@ | ||
| def pathbam = "file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/" | ||
| def pathgenome = "file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/" | ||
| // positions and essential parameters | ||
| def posfile = "${pathgenome}dbsnp_138.hg38.first_10_biallelic_sites.tsv', checkIfExists: true)" | ||
| def stitch_params = "[ [ id: 'test_positions' ], $posfile, [], [], 'chr21', 2, 1 ]" | ||
|
|
||
| // sequencing data in cram format | ||
| def crams_val = "[${pathbam}cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), ${pathbam}cram/test2.paired_end.recalibrated.sorted.cram', checkIfExists: true)]" | ||
| def crais_val = "[${pathbam}cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), ${pathbam}cram/test2.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true)]" | ||
| def reads_cram = "[ [ id: 'test_reads' ], $crams_val, $crais_val ]" | ||
|
|
||
| // sequencing data in bam format | ||
| def bams_val = "[${pathbam}bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), ${pathbam}bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true)]" | ||
| def bais_val = "[${pathbam}bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), ${pathbam}bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)]" | ||
| def reads_bam = "[ [ id:'test_reads' ], $bams_val, $bais_val ]" | ||
|
|
||
| // reference genome | ||
| def reference = "[[ id:'test_reference' ], ${pathgenome}genome.fasta', checkIfExists: true), ${pathgenome}genome.fasta.fai', checkIfExists: true)]" | ||
|
|
||
| // for reproducibility | ||
| def seed = 1 | ||
|
|
||
| nextflow_process { | ||
| name "Test Process STITCH" | ||
| script "../main.nf" | ||
| process "STITCH" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "stitch" | ||
|
|
||
| test("test_no_seed") { | ||
| when { | ||
| process { | ||
| """ | ||
| filelist = Channel.fromPath( $crams_val ) | ||
| .map { it[-1] as String } // get only filename | ||
| .collectFile( name: "cramlist.txt", newLine: true, sort: true ) | ||
| input[0] = Channel.of( $reads_cram ).combine( filelist ) | ||
| input[1] = $stitch_params | ||
| input[2] = $reference | ||
| input[3] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.input.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.rdata.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.plots.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.vcf.collect{ file(it[1]).name }, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test_with_seed") { | ||
| when { | ||
| process { | ||
| """ | ||
| filelist = Channel.fromPath( $crams_val ) | ||
| .map { it[-1] as String } // get only filename | ||
| .collectFile( name: "cramlist.txt", newLine: true, sort: true ) | ||
| input[0] = Channel.of( $reads_cram ).combine( filelist ) | ||
| input[1] = $stitch_params | ||
| input[2] = $reference | ||
| input[3] = $seed | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.input.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.rdata.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.plots.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.vcf.collect{ file(it[1]).name }, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test_two_stage_imputation") { | ||
| setup { | ||
| run ("STITCH", alias: "STITCH_GENERATE_INPUTS") { | ||
| script "../main.nf" | ||
| config "./stitch_generate_input.config" | ||
| process { | ||
| """ | ||
| filelist = Channel.fromPath( $crams_val ) | ||
| .map { it[-1] as String } // get only filename | ||
| .collectFile( name: "cramlist.txt", newLine: true, sort: true ) | ||
| input[0] = Channel.of( $reads_cram ).combine( filelist ) | ||
| input[1] = $stitch_params | ||
| input[2] = $reference | ||
| input[3] = $seed | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| config "./stitch_impute_only.config" | ||
| process { | ||
| """ | ||
| ch_input_2step = Channel.of( $stitch_params ) | ||
| .map { | ||
| meta, positions, target, rdata, chromosome_name, K, nGen -> | ||
| [ meta, positions ] | ||
| } | ||
| .combine( | ||
| STITCH_GENERATE_INPUTS.out.input | ||
| .join ( STITCH_GENERATE_INPUTS.out.rdata ) | ||
| ) | ||
| .map { | ||
| meta, positions, metaT, target, rdata -> | ||
| [ metaT, positions, target, rdata, "chr21", 2, 1 ] | ||
| } | ||
| input[0] = [[id: null], [], [], []] | ||
| input[1] = ch_input_2step | ||
| input[2] = [[id: null], [], []] | ||
| input[3] = $seed | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.input.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.rdata.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.plots.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.vcf.collect{ file(it[1]).name }, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test_with_bam") { | ||
| when { | ||
| process { | ||
| """ | ||
| filelist = Channel.fromPath( $bams_val ) | ||
| .map { it[-1] as String } // get only filename | ||
| .collectFile( name: "cramlist.txt", newLine: true, sort: true ) | ||
| input[0] = Channel.of( $reads_bam ).combine( filelist ) | ||
| input[1] = $stitch_params | ||
| input[2] = $reference | ||
| input[3] = $seed | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.input.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.rdata.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.plots.collect{ file(it[1]).listFiles().sort().name }, | ||
| process.out.vcf.collect{ file(it[1]).name }, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| } |
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