diff --git a/modules/nf-core/stitch/environment.yml b/modules/nf-core/stitch/environment.yml index 039968d65c9..4978bec281f 100644 --- a/modules/nf-core/stitch/environment.yml +++ b/modules/nf-core/stitch/environment.yml @@ -2,4 +2,7 @@ channels: - conda-forge - bioconda dependencies: + - conda-forge::r-base=4.3.1 + - conda-forge::rsync=3.2.7 - bioconda::r-stitch=1.6.10 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/stitch/main.nf b/modules/nf-core/stitch/main.nf index 2f76987f9ab..0f8d8109dd2 100644 --- a/modules/nf-core/stitch/main.nf +++ b/modules/nf-core/stitch/main.nf @@ -8,8 +8,8 @@ process STITCH { 'biocontainers/r-stitch:1.6.10--r43h06b5641_0' }" input: - tuple val(meta) , path(posfile), path(input, stageAs: "input"), path(rdata, stageAs: "RData_in"), val(chromosome_name), val(K), val(nGen) - tuple val(meta2), path(collected_crams), path(collected_crais), path(cramlist) + tuple val(meta), path(collected_crams), path(collected_crais), path(cramlist) + tuple val(meta2), path(posfile), path(input, stageAs: "input"), path(rdata, stageAs: "RData_in"), val(chromosome_name), val(K), val(nGen) tuple val(meta3), path(fasta), path(fasta_fai) val seed diff --git a/modules/nf-core/stitch/meta.yml b/modules/nf-core/stitch/meta.yml index 48a21c4996f..0035d34696e 100644 --- a/modules/nf-core/stitch/meta.yml +++ b/modules/nf-core/stitch/meta.yml @@ -23,6 +23,24 @@ tools: identifier: biotools:stitch-snijderlab input: - - meta: + type: map + description: | + Groovy Map containing information about the set of samples + e.g. `[ id:'test' ]` + - collected_crams: + type: file + description: List of sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - collected_crais: + type: file + description: List of BAM/CRAM/SAM index files + pattern: "*.{bai,crai,sai}" + - cramlist: + type: file + description: | + Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path. + pattern: "*.txt" + - - meta2: type: map description: | Groovy Map containing information about the set of positions to run the imputation over @@ -55,24 +73,6 @@ input: description: Number of generations since founding of the population to use for imputation. Refer to the documentation for the `--nGen` argument of STITCH for more information. - - - meta2: - type: map - description: | - Groovy Map containing information about the set of samples - e.g. `[ id:'test' ]` - - collected_crams: - type: file - description: List of sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - collected_crais: - type: file - description: List of BAM/CRAM/SAM index files - pattern: "*.{bai,crai,sai}" - - cramlist: - type: file - description: | - Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path. - pattern: "*.txt" - - meta3: type: map description: | diff --git a/modules/nf-core/stitch/tests/main.nf.test b/modules/nf-core/stitch/tests/main.nf.test new file mode 100644 index 00000000000..9a7d1803302 --- /dev/null +++ b/modules/nf-core/stitch/tests/main.nf.test @@ -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() } + ) + } + } + +} diff --git a/modules/nf-core/stitch/tests/main.nf.test.snap b/modules/nf-core/stitch/tests/main.nf.test.snap new file mode 100644 index 00000000000..ee28277fbcd --- /dev/null +++ b/modules/nf-core/stitch/tests/main.nf.test.snap @@ -0,0 +1,170 @@ +{ + "test_with_bam": { + "content": [ + [ + [ + "sample.1.input.chr21.RData", + "sample.2.input.chr21.RData" + ] + ], + [ + [ + "EM.all.chr21.RData", + "end.chr21.RData", + "endEM.chr21.RData", + "sampleNames.chr21.RData", + "start.chr21.RData", + "startEM.chr21.RData" + ] + ], + [ + [ + "alphaMat.chr21.all.s.1.png", + "alphaMat.chr21.normalized.s.1.png", + "hapSum.chr21.s.1.png", + "hapSum_log.chr21.s.1.png", + "metricsForPostImputationQC.chr21.sample.jpg", + "metricsForPostImputationQCChromosomeWide.chr21.sample.jpg", + "r2.chr21.goodonly.jpg" + ] + ], + [ + "stitch.chr21.vcf.gz" + ], + [ + "versions.yml:md5,23ba0a3cec10c1bdb411b3e1f31b008e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-22T20:16:19.412761604" + }, + "test_no_seed": { + "content": [ + [ + [ + "sample.1.input.chr21.RData", + "sample.2.input.chr21.RData" + ] + ], + [ + [ + "EM.all.chr21.RData", + "end.chr21.RData", + "endEM.chr21.RData", + "sampleNames.chr21.RData", + "start.chr21.RData", + "startEM.chr21.RData" + ] + ], + [ + [ + "alphaMat.chr21.all.s.1.png", + "alphaMat.chr21.normalized.s.1.png", + "hapSum.chr21.s.1.png", + "hapSum_log.chr21.s.1.png", + "metricsForPostImputationQC.chr21.sample.jpg", + "metricsForPostImputationQCChromosomeWide.chr21.sample.jpg", + "r2.chr21.goodonly.jpg" + ] + ], + [ + "stitch.chr21.vcf.gz" + ], + [ + "versions.yml:md5,23ba0a3cec10c1bdb411b3e1f31b008e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-22T18:49:25.941823568" + }, + "test_two_stage_imputation": { + "content": [ + [ + [ + "sample.1.input.chr21.RData", + "sample.2.input.chr21.RData" + ] + ], + [ + [ + "EM.all.chr21.RData", + "end.chr21.RData", + "endEM.chr21.RData", + "sampleNames.chr21.RData", + "start.chr21.RData", + "startEM.chr21.RData" + ] + ], + [ + [ + "alphaMat.chr21.all.s.1.png", + "alphaMat.chr21.normalized.s.1.png", + "hapSum.chr21.s.1.png", + "hapSum_log.chr21.s.1.png", + "metricsForPostImputationQC.chr21.sample.jpg", + "metricsForPostImputationQCChromosomeWide.chr21.sample.jpg", + "r2.chr21.goodonly.jpg" + ] + ], + [ + "stitch.chr21.vcf.gz" + ], + [ + "versions.yml:md5,019f1127aacfb7d14a0c4ae3d740a07d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-22T20:14:01.151837306" + }, + "test_with_seed": { + "content": [ + [ + [ + "sample.1.input.chr21.RData", + "sample.2.input.chr21.RData" + ] + ], + [ + [ + "EM.all.chr21.RData", + "end.chr21.RData", + "endEM.chr21.RData", + "sampleNames.chr21.RData", + "start.chr21.RData", + "startEM.chr21.RData" + ] + ], + [ + [ + "alphaMat.chr21.all.s.1.png", + "alphaMat.chr21.normalized.s.1.png", + "hapSum.chr21.s.1.png", + "hapSum_log.chr21.s.1.png", + "metricsForPostImputationQC.chr21.sample.jpg", + "metricsForPostImputationQCChromosomeWide.chr21.sample.jpg", + "r2.chr21.goodonly.jpg" + ] + ], + [ + "stitch.chr21.vcf.gz" + ], + [ + "versions.yml:md5,23ba0a3cec10c1bdb411b3e1f31b008e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-22T18:59:46.592393397" + } +} \ No newline at end of file diff --git a/modules/nf-core/stitch/tests/stitch_generate_input.config b/modules/nf-core/stitch/tests/stitch_generate_input.config new file mode 100644 index 00000000000..3e0a5666f07 --- /dev/null +++ b/modules/nf-core/stitch/tests/stitch_generate_input.config @@ -0,0 +1,6 @@ +process { + withName: STITCH_GENERATE_INPUTS { + ext.args2 = "--generateInputOnly TRUE" + } +} + diff --git a/modules/nf-core/stitch/tests/stitch_impute_only.config b/modules/nf-core/stitch/tests/stitch_impute_only.config new file mode 100644 index 00000000000..f3304ceac7e --- /dev/null +++ b/modules/nf-core/stitch/tests/stitch_impute_only.config @@ -0,0 +1,5 @@ +process { + withName: STITCH { + ext.args2 = "--regenerateInputWithDefaultValues TRUE" + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index c1242df8247..5f98df7f0fd 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -636,9 +636,6 @@ srst2/srst2: stecfinder: - modules/nf-core/stecfinder/** - tests/modules/nf-core/stecfinder/** -stitch: - - modules/nf-core/stitch/** - - tests/modules/nf-core/stitch/** subworkflows/align_bowtie2: - subworkflows/nf-core/align_bowtie2/** - tests/subworkflows/nf-core/align_bowtie2/** diff --git a/tests/modules/nf-core/stitch/main.nf b/tests/modules/nf-core/stitch/main.nf deleted file mode 100644 index e98b7438cbe..00000000000 --- a/tests/modules/nf-core/stitch/main.nf +++ /dev/null @@ -1,135 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { STITCH as STITCH_ONE_STEP } from '../../../../modules/nf-core/stitch/main.nf' -include { STITCH as STITCH_GENERATE_INPUTS } from '../../../../modules/nf-core/stitch/main.nf' -include { STITCH as STITCH_IMPUTE_ONLY } from '../../../../modules/nf-core/stitch/main.nf' - -// positions and essential parameters -def posfile = file(params.test_data['homo_sapiens']['genome']['genome_21_stitch_posfile'], checkIfExists: true) -def input_empty = [] -def rdata_empty = [] -def chromosome_name_val = "chr21" -def K_val = 2 -def nGen_val = 1 -def stitch_input = [ [ id: "test_positions" ], posfile, input_empty, rdata_empty, chromosome_name_val, K_val, nGen_val ] - -// sequencing data in cram format -def crams_val = [ - params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram' ], - params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], -] -def crais_val = [ - params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai' ], - params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], -] -def reads = [ [ id:"test_reads" ], crams_val, crais_val ] - -// sequencing data in bam format -def bams_val = [ - params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam' ], - params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], -] -def bais_val = [ - params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai' ], - params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], -] -def reads_bam = [ [ id:"test_reads" ], bams_val, bais_val ] - -// reference genome -def reference = [ - [ id:"test_reference" ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'] , checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true), -] - -// for reproducibility -def seed = 1 - -// -// Test workflows -// - -workflow GET_READS { - main: - cramlist = Channel.fromPath( crams_val ) - .map { it[-1] as String } // get only filename - .collectFile( name: "cramlist.txt", newLine: true, sort: true ) - - - emit: - Channel.of( reads ).combine( cramlist ).first() -} - -workflow GET_READS_BAM { - main: - bamlist = Channel.fromPath( bams_val ) - .map { it[-1] as String } // get only filename - .collectFile( name: "bamlist.txt", newLine: true, sort: true ) - - - emit: - Channel.of( reads_bam ).combine( bamlist ).first() -} - - -workflow test_with_seed { - GET_READS() - STITCH_ONE_STEP ( - stitch_input, - GET_READS.out, - reference, - seed, - ) -} - -workflow test_no_seed { - GET_READS() - STITCH_ONE_STEP ( - stitch_input, - GET_READS.out, - reference, - [], - ) -} - -workflow test_two_stage_imputation { - GET_READS() - STITCH_GENERATE_INPUTS ( - stitch_input, - GET_READS.out, - reference, - seed, - ) - - Channel.of( stitch_input ) - .map { - meta, positions, input, rdata, chromosome_name, K, nGen -> - [ meta, positions ] - } - .join ( STITCH_GENERATE_INPUTS.out.input ) - .join ( STITCH_GENERATE_INPUTS.out.rdata ) - .map { - meta, positions, input, rdata -> - [ meta, positions, input, rdata, chromosome_name_val, K_val, nGen_val ] - } - .set { stitch_input_second_step } - - STITCH_IMPUTE_ONLY( - stitch_input_second_step, - [[id: null], [], [], []], - [[id: null], [], []], - seed, - ) -} - -workflow test_bam { - GET_READS_BAM() - STITCH_ONE_STEP ( - stitch_input, - GET_READS_BAM.out, - reference, - seed, - ) -} diff --git a/tests/modules/nf-core/stitch/nextflow.config b/tests/modules/nf-core/stitch/nextflow.config deleted file mode 100644 index 89433c53f2a..00000000000 --- a/tests/modules/nf-core/stitch/nextflow.config +++ /dev/null @@ -1,12 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: STITCH_GENERATE_INPUTS { - ext.args2 = "--generateInputOnly TRUE" - } - withName: STITCH_IMPUTE_ONLY { - ext.args2 = "--regenerateInputWithDefaultValues TRUE" - } - -} diff --git a/tests/modules/nf-core/stitch/test.yml b/tests/modules/nf-core/stitch/test.yml deleted file mode 100644 index aec395e046e..00000000000 --- a/tests/modules/nf-core/stitch/test.yml +++ /dev/null @@ -1,109 +0,0 @@ -- name: stitch test_with_seed - command: nextflow run ./tests/modules/nf-core/stitch -entry test_with_seed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stitch/nextflow.config - tags: - - stitch - files: - - path: output/stitch/RData/EM.all.chr21.RData - md5sum: 41d63ae9ba7696e97ce7e3dafd1454ea - - path: output/stitch/RData/sampleNames.chr21.RData - md5sum: df745cab2454edcdafc0825136f17664 - - path: output/stitch/RData/start.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/end.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/startEM.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/endEM.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/input/sample.1.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/input/sample.2.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/plots/alphaMat.chr21.all.s.1.png - - path: output/stitch/plots/alphaMat.chr21.normalized.s.1.png - - path: output/stitch/plots/hapSum.chr21.s.1.png - - path: output/stitch/plots/hapSum_log.chr21.s.1.png - - path: output/stitch/plots/metricsForPostImputationQC.chr21.sample.jpg - - path: output/stitch/plots/metricsForPostImputationQCChromosomeWide.chr21.sample.jpg - - path: output/stitch/plots/r2.chr21.goodonly.jpg - - path: output/stitch/stitch.chr21.vcf.gz - md5sum: a7650b4053d0f6abb675a4763d73626f - - path: output/stitch/versions.yml - -- name: stitch test_no_seed - command: nextflow run ./tests/modules/nf-core/stitch -entry test_no_seed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stitch/nextflow.config - tags: - - stitch - files: - - path: output/stitch/RData/EM.all.chr21.RData - - path: output/stitch/RData/sampleNames.chr21.RData - md5sum: df745cab2454edcdafc0825136f17664 - - path: output/stitch/RData/start.chr21.RData - - path: output/stitch/RData/end.chr21.RData - - path: output/stitch/RData/startEM.chr21.RData - - path: output/stitch/RData/endEM.chr21.RData - - path: output/stitch/input/sample.1.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/input/sample.2.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/plots/alphaMat.chr21.all.s.1.png - - path: output/stitch/plots/alphaMat.chr21.normalized.s.1.png - - path: output/stitch/plots/hapSum.chr21.s.1.png - - path: output/stitch/plots/hapSum_log.chr21.s.1.png - - path: output/stitch/plots/metricsForPostImputationQC.chr21.sample.jpg - - path: output/stitch/plots/metricsForPostImputationQCChromosomeWide.chr21.sample.jpg - - path: output/stitch/plots/r2.chr21.goodonly.jpg - - path: output/stitch/stitch.chr21.vcf.gz - - path: output/stitch/versions.yml - -- name: stitch test_two_stage_imputation - command: nextflow run ./tests/modules/nf-core/stitch -entry test_two_stage_imputation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stitch/nextflow.config - tags: - - stitch - files: - - path: output/stitch/RData/EM.all.chr21.RData - md5sum: 41d63ae9ba7696e97ce7e3dafd1454ea - - path: output/stitch/RData/sampleNames.chr21.RData - md5sum: df745cab2454edcdafc0825136f17664 - - path: output/stitch/RData/start.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/end.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/startEM.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/endEM.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/input/sample.1.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/input/sample.2.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/plots/alphaMat.chr21.all.s.1.png - - path: output/stitch/plots/alphaMat.chr21.normalized.s.1.png - - path: output/stitch/plots/hapSum.chr21.s.1.png - - path: output/stitch/plots/hapSum_log.chr21.s.1.png - - path: output/stitch/plots/metricsForPostImputationQC.chr21.sample.jpg - - path: output/stitch/plots/metricsForPostImputationQCChromosomeWide.chr21.sample.jpg - - path: output/stitch/plots/r2.chr21.goodonly.jpg - - path: output/stitch/stitch.chr21.vcf.gz - md5sum: a7650b4053d0f6abb675a4763d73626f - - path: output/stitch/versions.yml - -- name: stitch test_bam - command: nextflow run ./tests/modules/nf-core/stitch -entry test_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stitch/nextflow.config - tags: - - stitch - files: - - path: output/stitch/RData/EM.all.chr21.RData - md5sum: 41d63ae9ba7696e97ce7e3dafd1454ea - - path: output/stitch/RData/sampleNames.chr21.RData - md5sum: df745cab2454edcdafc0825136f17664 - - path: output/stitch/RData/start.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/end.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/startEM.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/RData/endEM.chr21.RData # it contains the execution time so md5 checkusm not possible even with seed - - path: output/stitch/input/sample.1.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/input/sample.2.input.chr21.RData - md5sum: 39741bab12230d0cfcbff64621708da0 - - path: output/stitch/plots/alphaMat.chr21.all.s.1.png - - path: output/stitch/plots/alphaMat.chr21.normalized.s.1.png - - path: output/stitch/plots/hapSum.chr21.s.1.png - - path: output/stitch/plots/hapSum_log.chr21.s.1.png - - path: output/stitch/plots/metricsForPostImputationQC.chr21.sample.jpg - - path: output/stitch/plots/metricsForPostImputationQCChromosomeWide.chr21.sample.jpg - - path: output/stitch/plots/r2.chr21.goodonly.jpg - - path: output/stitch/stitch.chr21.vcf.gz - md5sum: a7650b4053d0f6abb675a4763d73626f - - path: output/stitch/versions.yml