diff --git a/assets/hlahd_software_meta.json b/assets/hlahd_software_meta.json deleted file mode 100644 index 41d3ff0..0000000 --- a/assets/hlahd_software_meta.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "hlahd": { - "version": "1.7.1", - "software_md5": "44f0185f514f026fdd709fb34743980a" - } -} diff --git a/assets/software_meta.json b/assets/software_meta.json new file mode 100644 index 0000000..1d0385f --- /dev/null +++ b/assets/software_meta.json @@ -0,0 +1,11 @@ +{ + "hlahd": { + "version": "1.7.1", + "software_md5": "44f0185f514f026fdd709fb34743980a" + }, + "hlala": { + "graph": "PRG_MHC_GRCh38_withIMGT", + "graph_url": "https://www.well.ox.ac.uk/downloads/HLA-LA/graphs/PRG_MHC_GRCh38_withIMGT.tar.gz", + "graph_md5": "525a8aa0c7f357bf29fe2c75ef1d477d" + } +} diff --git a/conf/modules.config b/conf/modules.config index 8b52f00..d0c537f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -20,18 +20,20 @@ process { withName: CHECK_PAIRED { ext.args = '' + publishDir = [ enabled: false ] } withName: FASTQC { ext.args = '--quiet' } + withName: YARA_INDEX { + publishDir = [ enabled: false ] + } + withName: YARA_MAPPER { ext.args = '-e 3' - publishDir = [ - path: { "${params.outdir}/yara/${meta.id}" }, - mode: params.publish_dir_mode - ] + publishDir = [ enabled: false ] } withName: OPTITYPE { @@ -44,6 +46,10 @@ process { ext.args2 = "solver=${params.solver}" } + withName: 'HLAHD_INSTALL' { + publishDir = [ enabled: false ] + } + withName: HLAHD { ext.args = '-m 50' publishDir = [ @@ -53,6 +59,31 @@ process { ] } + withName: 'HLALA_TYPING' { + ext.args = '--graph PRG_MHC_GRCh38_withIMGT' + publishDir = [ + path: { "${params.outdir}/hlala/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + + withName: 'SAMTOOLS_VIEW' { + ext.args = '--output-fmt bam' // Ensure BGZF-compressed BAM output + ext.prefix = { "${meta.id}.hlala" } + publishDir = [ + enabled: false + ] + } + + withName: 'HLALA_DOWNLOAD' { + publishDir = [ enabled: false ] + } + + withName: 'SAMTOOLS_COLLATEFASTQ' { + publishDir = [ enabled: false ] + } + withName: CAT_FASTQ { publishDir = [ path: { params.save_merged_fastq ? "${params.outdir}/fastq" : params.outdir }, diff --git a/conf/test_hlala.config b/conf/test_hlala.config new file mode 100644 index 0000000..34e4960 --- /dev/null +++ b/conf/test_hlala.config @@ -0,0 +1,33 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running HLA*LA tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines bundled input files and everything required to run a fast and simple test. + + Use as follows: + nextflow run nf-core/hlatyping -profile test_hlala, --outdir + + Note: HLA*LA requires a pre-built graph directory. If hlala_graph_dir is not provided, + the tool will attempt to download and build it automatically (requires significant + time and resources on first run). +---------------------------------------------------------------------------------------- + */ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '6.h' + ] +} + +params { + config_profile_name = 'HLA*LA Test Profile' + config_profile_description = 'Test dataset with BAM files using HLA*LA' + + // Input data - HLA*LA requires pre-aligned BAM files + input = params.pipelines_testdata_base_path + 'hlatyping/samplesheets/samplesheet_bam.csv' + tools = 'hlala' + + // HLA*LA graph directory - if not set, graph will be downloaded automatically +} diff --git a/conf/test_optitype_hlala.config b/conf/test_optitype_hlala.config new file mode 100644 index 0000000..b6a9fcc --- /dev/null +++ b/conf/test_optitype_hlala.config @@ -0,0 +1,32 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running OptiType + HLA*LA tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines bundled input files and everything required to run a fast and simple test. + + Use as follows: + nextflow run nf-core/hlatyping -profile test_optitype_hlala, --outdir +---------------------------------------------------------------------------------------- + */ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'OptiType + HLA*LA Test Profile' + config_profile_description = 'Test dataset with BAM files using both OptiType and HLA*LA' + + // Input data - HLA*LA requires pre-aligned BAM files + input = params.pipelines_testdata_base_path + 'hlatyping/samplesheets/samplesheet_bam.csv' + // Parent directory containing the graph (e.g., graphs/PRG_MHC_GRCh38_withIMGT/) + hlala_graph_dir = "${projectDir}/graphs" + tools = 'optitype,hlala' + + // OptiType parameters + solver = 'glpk' +} diff --git a/modules.json b/modules.json index 087012a..835adca 100644 --- a/modules.json +++ b/modules.json @@ -20,6 +20,16 @@ "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, + "hlala/preparegraph": { + "branch": "master", + "git_sha": "5e748ff2b0f990949081c9e49792622eb3fe9ee9", + "installed_by": ["modules"] + }, + "hlala/typing": { + "branch": "master", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "installed_by": ["modules"] + }, "multiqc": { "branch": "master", "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", diff --git a/modules/local/hlala/download/main.nf b/modules/local/hlala/download/main.nf new file mode 100644 index 0000000..b5aa9b4 --- /dev/null +++ b/modules/local/hlala/download/main.nf @@ -0,0 +1,60 @@ +process HLALA_DOWNLOAD { + tag "$graph_name" + label 'process_single' + + conda "conda-forge::wget=1.21.4 conda-forge::coreutils=9.5" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/wget:1.21.4' : + 'biocontainers/wget:1.21.4' }" + + input: + tuple val(graph_name), val(graph_url), val(graph_md5), path(graph_tarball) + + output: + path "graphs", emit: graph + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def use_local = graph_tarball.name != 'NO_FILE' + """ + if [ "${use_local}" = "true" ]; then + # Use provided tarball + TARBALL="${graph_tarball}" + else + # Download graph + wget -q "${graph_url}" -O ${graph_name}.tar.gz + TARBALL="${graph_name}.tar.gz" + fi + + # Verify MD5 checksum + checksum="\$(md5sum "\$TARBALL" | cut -f1 -d' ')" + if [ "\$checksum" != "${graph_md5}" ]; then + echo "Checksum error: expected ${graph_md5}, got \$checksum" >&2 + exit 2 + fi + + # Extract into parent directory structure for HLA*LA --customGraphDir + mkdir -p graphs + tar -xzf "\$TARBALL" -C graphs + [ "${use_local}" = "false" ] && rm "\$TARBALL" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + wget: \$(wget --version 2>&1 | head -1 | sed 's/GNU Wget //;s/ .*//') + END_VERSIONS + """ + + stub: + """ + mkdir -p graphs/${graph_name} + touch graphs/${graph_name}/serializedGRAPH + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + wget: \$(wget --version 2>&1 | head -1 | sed 's/GNU Wget //;s/ .*//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/hlala/preparegraph/environment.yml b/modules/nf-core/hlala/preparegraph/environment.yml new file mode 100644 index 0000000..029d7a4 --- /dev/null +++ b/modules/nf-core/hlala/preparegraph/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::hla-la=1.0.4 diff --git a/modules/nf-core/hlala/preparegraph/main.nf b/modules/nf-core/hlala/preparegraph/main.nf new file mode 100644 index 0000000..c2db328 --- /dev/null +++ b/modules/nf-core/hlala/preparegraph/main.nf @@ -0,0 +1,85 @@ +process HLALA_PREPAREGRAPH { + tag "$meta.id" + label 'process_high' + stageInMode 'copy' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/hla-la:1.0.4--h077b44d_1': + 'biocontainers/hla-la:1.0.4--h077b44d_1' }" + + input: + tuple val(meta), path(graph) + + output: + tuple val(meta), path("${graph}") , emit: graph + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def bin = "" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + bin="\$CONDA_PREFIX/opt/hla-la/bin/HLA-LA" + } else { + bin="/usr/local/opt/hla-la/bin/HLA-LA" + } + + """ + ${bin} \\ + --action prepareGraph \\ + --PRG_graph_dir $graph + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hlala: 1.0.3 + END_VERSIONS + """ + + stub: + """ + mkdir -p ${graph}/translation + mkdir -p ${graph}/mapping_PRGonly + mkdir -p ${graph}/referenceGenomeSimulations + mkdir -p ${graph}/extendedReferenceGenome + mkdir -p ${graph}/sampledReferenceGenomes + mkdir -p ${graph}/knownReferences + mkdir -p ${graph}/mapping + mkdir -p ${graph}/PRG + + touch ${graph}/translation/100.txt + touch ${graph}/mapping_PRGonly/referenceGenome.fa_bowtie2idx.1.bt2 + touch ${graph}/mapping_PRGonly/referenceGenome.fa_bowtie2idx.3.bt2 + touch ${graph}/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.2.bt2 + touch ${graph}/mapping_PRGonly/check_refSequence_length.pl + touch ${graph}/mapping_PRGonly/referenceGenome.fa_bowtie2idx.2.bt2 + touch ${graph}/mapping_PRGonly/referenceGenome.fa.amb + touch ${graph}/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.1.bt2 + touch ${graph}/mapping_PRGonly/referenceGenome.fa.bwt + touch ${graph}/mapping_PRGonly/referenceGenome.fa.pac + touch ${graph}/mapping_PRGonly/referenceGenome.fa + touch ${graph}/mapping_PRGonly/referenceGenome.fa.sa + touch ${graph}/mapping_PRGonly/referenceGenome.fa.ann + touch ${graph}/mapping_PRGonly/referenceGenome.fa_bowtie2idx.4.bt2 + touch ${graph}/extendedReferenceGenome/extendedReferenceGenome.fa + touch ${graph}/serializedGRAPH_preGapPathIndex + touch ${graph}/knownReferences/1000G_B38.txt + touch ${graph}/knownReferences/1000G_B37_noChr.txt + touch ${graph}/knownReferences/PRG_MHC_GRCh38_withIMGT.txt + touch ${graph}/knownReferences/B37_generic_noChr.txt + touch ${graph}/mapping/100.fa + touch ${graph}/sequences.txt + touch ${graph}/serializedGRAPH + touch ${graph}/PRG/100_gene_HLA-A_9_exon_5.txt + touch ${graph}/PRG/100_gene_HLA-A_9_exon_5.txt.graph + touch ${graph}/PRG/graph.txt + touch ${graph}/PRG/segments.txt + touch ${graph}/PRG/positions.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hlala: 1.0.3 + END_VERSIONS + """ +} diff --git a/modules/nf-core/hlala/preparegraph/meta.yml b/modules/nf-core/hlala/preparegraph/meta.yml new file mode 100644 index 0000000..bdda999 --- /dev/null +++ b/modules/nf-core/hlala/preparegraph/meta.yml @@ -0,0 +1,46 @@ +name: "hlala_preparegraph" +description: Pre-compute the graph index structure. +keywords: + - hla + - hlala + - hla_typing + - hlala_typing +tools: + - "hlala": + description: "HLA typing from short and long reads" + homepage: "https://github.com/DiltheyLab/HLA-LA" + documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala" + tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" + doi: "10.1093/bioinformatics/btz235" + licence: ["GPL"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: directory + description: PRG graph directory +output: + graph: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${graph}: + type: directory + description: PRG graph directory + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@mapo9" +maintainers: + - "@mapo9" diff --git a/modules/nf-core/hlala/preparegraph/tests/main.nf.test b/modules/nf-core/hlala/preparegraph/tests/main.nf.test new file mode 100644 index 0000000..429e32a --- /dev/null +++ b/modules/nf-core/hlala/preparegraph/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process HLALA_PREPAREGRAPH" + script "../main.nf" + process "HLALA_PREPAREGRAPH" + + tag "modules" + tag "modules_nfcore" + tag "hlala" + tag "hlala/preparegraph" + tag "unzip" + + test("homo_sapiens - prg") { + config "./nextflow.config" + + setup { + + run("UNZIP"){ + script "../../../unzip/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/PRG_test.zip', checkIfExists: true) + ] + """ + } + } + } + when { + process { + """ + input[0] = UNZIP.out.unzipped_archive.map{ meta, filepath -> + [meta, "\$filepath/PRG_\${filepath.toString().split("/").last()}"] + } + """ + } + } + + then { + def stable_name = getAllFilesFromDir(outputDir, relative:true, includeDir: true) + def stable_content = getAllFilesFromDir(outputDir, ignore: ['**/referenceGenome.fa.{bwt,pac,sa}','**/referenceGenome.fa_bowtie2idx*']) + assertAll( + { assert process.success }, + { assert snapshot(stable_name,stable_content).match() } + ) + } + + } + + test("homo_sapiens - prg - stub") { + + options "-stub" + setup { + + run("UNZIP"){ + script "../../../unzip/main.nf" + options "-stub" + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/PRG_test.zip', checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = UNZIP.out.unzipped_archive + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap b/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap new file mode 100644 index 0000000..f982227 --- /dev/null +++ b/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap @@ -0,0 +1,269 @@ +{ + "homo_sapiens - prg - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + [ + "100_gene_HLA-A_9_exon_5.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "100_gene_HLA-A_9_exon_5.txt.graph:md5,d41d8cd98f00b204e9800998ecf8427e", + "graph.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "positions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "segments.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + 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"hlala/PRG_test/translation/100.txt", + "hlala/versions.yml", + "unzip", + "unzip/test", + "unzip/test/PRG_test", + "unzip/test/PRG_test/.nextflow", + "unzip/test/PRG_test/.nextflow.log", + "unzip/test/PRG_test/.nextflow/plr", + "unzip/test/PRG_test/PRG", + "unzip/test/PRG_test/PRG/100_gene_HLA-A_9_exon_5.txt", + "unzip/test/PRG_test/PRG/100_gene_HLA-A_9_exon_5.txt.graph", + "unzip/test/PRG_test/PRG/graph.txt", + "unzip/test/PRG_test/PRG/positions.txt", + "unzip/test/PRG_test/PRG/segments.txt", + "unzip/test/PRG_test/extendedReferenceGenome", + "unzip/test/PRG_test/extendedReferenceGenome/extendedReferenceGenome.fa", + "unzip/test/PRG_test/knownReferences", + "unzip/test/PRG_test/knownReferences/1000G_B37_noChr.txt", + "unzip/test/PRG_test/knownReferences/1000G_B38.txt", + "unzip/test/PRG_test/knownReferences/B37_generic_noChr.txt", + "unzip/test/PRG_test/knownReferences/PRG_MHC_GRCh38_withIMGT.txt", + "unzip/test/PRG_test/mapping", + "unzip/test/PRG_test/mapping/100.fa", + "unzip/test/PRG_test/mapping_PRGonly", + "unzip/test/PRG_test/mapping_PRGonly/check_refSequence_length.pl", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.amb", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.ann", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.bwt", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.pac", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa.sa", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.1.bt2", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.2.bt2", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.3.bt2", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.4.bt2", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.1.bt2", + "unzip/test/PRG_test/mapping_PRGonly/referenceGenome.fa_bowtie2idx.rev.2.bt2", + "unzip/test/PRG_test/referenceGenomeSimulations", + "unzip/test/PRG_test/sampledReferenceGenomes", + "unzip/test/PRG_test/sequences.txt", + "unzip/test/PRG_test/serializedGRAPH", + "unzip/test/PRG_test/serializedGRAPH_preGapPathIndex", + "unzip/test/PRG_test/translation", + "unzip/test/PRG_test/translation/100.txt", + "unzip/versions.yml" + ], + [ + ".nextflow.log:md5,f22b6ca679424bea221fe100b4162b4a", + "100_gene_HLA-A_9_exon_5.txt:md5,fa4f97441bdd999f3ada1a49e67b726b", + "100_gene_HLA-A_9_exon_5.txt.graph:md5,0c5532614ffa94e30321c521e5a5046e", + "graph.txt:md5,434932977b863df94d3ada073b7636cf", + "positions.txt:md5,9f97b556f9ddf0414ffeaeb568bfb81f", + "segments.txt:md5,b60e45e75e63e5fde13bb9bea4a4a079", + "extendedReferenceGenome.fa:md5,c2e7c88c3ec5bfe966fb9204689dffc9", + "1000G_B37_noChr.txt:md5,df42b5bbf6a2de7c8a4fa0a04176b614", + "1000G_B38.txt:md5,252cc753ecdaf8e76102511d2ec7ff57", + "B37_generic_noChr.txt:md5,35652c6d147a3182d1e4dc11c88dc5af", + "PRG_MHC_GRCh38_withIMGT.txt:md5,c7750bb669e8d59409bc42202da3df75", + "100.fa:md5,ecbd3efeb988c3cf2d4e6d3ff2cd92c8", + "check_refSequence_length.pl:md5,ab1646b5838214ac4b1f902937a70967", + "referenceGenome.fa:md5,512b39c490d74bb91ce5ad1d8616e09e", + "referenceGenome.fa.amb:md5,7b847d4f48865b52f04cce82328199c1", + "referenceGenome.fa.ann:md5,c1943aa321630550d12a435e4350dfdc", + "sequences.txt:md5,61a3df2ca23dbe8d35c65944784def76", + "serializedGRAPH:md5,a88016a601377a967feb04c1bbeeba65", + "serializedGRAPH_preGapPathIndex:md5,65ea9cd52a00ffd51a2460c6887b277e", + "100.txt:md5,8dd91725d9a2f1f71a82ae1d190aa840", + "versions.yml:md5,f1108f072a11ccc5a063bf17a78ecd2d", + ".nextflow.log:md5,f22b6ca679424bea221fe100b4162b4a", + "100_gene_HLA-A_9_exon_5.txt:md5,fa4f97441bdd999f3ada1a49e67b726b", + "100_gene_HLA-A_9_exon_5.txt.graph:md5,0c5532614ffa94e30321c521e5a5046e", + "graph.txt:md5,434932977b863df94d3ada073b7636cf", + "positions.txt:md5,9f97b556f9ddf0414ffeaeb568bfb81f", + "segments.txt:md5,b60e45e75e63e5fde13bb9bea4a4a079", + "extendedReferenceGenome.fa:md5,c2e7c88c3ec5bfe966fb9204689dffc9", + "1000G_B37_noChr.txt:md5,df42b5bbf6a2de7c8a4fa0a04176b614", + "1000G_B38.txt:md5,252cc753ecdaf8e76102511d2ec7ff57", + "B37_generic_noChr.txt:md5,35652c6d147a3182d1e4dc11c88dc5af", + "PRG_MHC_GRCh38_withIMGT.txt:md5,c7750bb669e8d59409bc42202da3df75", + "100.fa:md5,ecbd3efeb988c3cf2d4e6d3ff2cd92c8", + "check_refSequence_length.pl:md5,ab1646b5838214ac4b1f902937a70967", + "referenceGenome.fa:md5,512b39c490d74bb91ce5ad1d8616e09e", + "referenceGenome.fa.amb:md5,7b847d4f48865b52f04cce82328199c1", + "referenceGenome.fa.ann:md5,c1943aa321630550d12a435e4350dfdc", + "sequences.txt:md5,61a3df2ca23dbe8d35c65944784def76", + "serializedGRAPH:md5,a88016a601377a967feb04c1bbeeba65", + "serializedGRAPH_preGapPathIndex:md5,65ea9cd52a00ffd51a2460c6887b277e", + "100.txt:md5,8dd91725d9a2f1f71a82ae1d190aa840", + "versions.yml:md5,52c55ce814e8bc9edc5a6c625ed794b8" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-03-26T10:50:11.256875" + } +} \ No newline at end of file diff --git a/modules/nf-core/hlala/preparegraph/tests/nextflow.config b/modules/nf-core/hlala/preparegraph/tests/nextflow.config new file mode 100644 index 0000000..7617e5b --- /dev/null +++ b/modules/nf-core/hlala/preparegraph/tests/nextflow.config @@ -0,0 +1,11 @@ +params { + outdir = "output/" +} + +process { + + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: 'copy' + ] +} diff --git a/modules/nf-core/hlala/typing/environment.yml b/modules/nf-core/hlala/typing/environment.yml new file mode 100644 index 0000000..029d7a4 --- /dev/null +++ b/modules/nf-core/hlala/typing/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::hla-la=1.0.4 diff --git a/modules/nf-core/hlala/typing/main.nf b/modules/nf-core/hlala/typing/main.nf new file mode 100644 index 0000000..91287ee --- /dev/null +++ b/modules/nf-core/hlala/typing/main.nf @@ -0,0 +1,155 @@ +process HLALA_TYPING { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/hla-la:1.0.4--h077b44d_1': + 'biocontainers/hla-la:1.0.4--h077b44d_1' }" + + input: + tuple val(meta), path(bam), path(bai), path(graph) + + output: + tuple val(meta), path("results") , emit: results + tuple val(meta), path("results/extraction.bam") , emit: extraction + tuple val(meta), path("results/extraction.bam.bai") , emit: extraction_index + tuple val(meta), path("results/extraction_mapped.bam") , emit: extraction_mapped + tuple val(meta), path("results/extraction_unmapped.bam") , emit: extraction_unmpapped + tuple val(meta), path("results/hla/*") , emit: hla + tuple val(meta), path("results/*.fastq") , emit: fastq + tuple val(meta), path("results/reads_per_level.txt") , emit: reads_per_level + tuple val(meta), path("results/remapped_with_a.bam") , emit: remapped + tuple val(meta), path("results/remapped_with_a.bam.bai") , emit: remapped_index + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + + def bin = "" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + bin="\$CONDA_PREFIX/opt/hla-la/src/HLA-LA.pl" + } else { + bin="/usr/local/opt/hla-la/src/HLA-LA.pl" + } + + """ + ${bin} \\ + --BAM $bam \\ + --customGraphDir ${graph} \\ + --sampleID $prefix \\ + --workingDir . \\ + --maxThreads $task.cpus \\ + $args + + mkdir -p results + mv ${prefix}/ results/ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hla-la: ${VERSION} + END_VERSIONS + """ + + stub: + def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + mkdir -p results + + touch results/R_1.fastq + touch results/R_2.fastq + touch results/R_U.fastq + touch results/extraction.bam + touch results/extraction.bam.bai + touch results/extraction_mapped.bam + touch results/extraction_unmapped.bam + touch results/remapped_with_a.bam + touch results/remapped_with_a.bam.bai + touch results/reads_per_level.txt + + mkdir results/hla + touch results/hla/histogram_matchesPerRead.txt + touch results/hla/R1_bestguess_G.txt + touch results/hla/R1_bestguess.txt + touch results/hla/R1_columnIncompatibilities_A.txt + touch results/hla/R1_columnIncompatibilities_B.txt + touch results/hla/R1_columnIncompatibilities_C.txt + touch results/hla/R1_columnIncompatibilities_DPA1.txt + touch results/hla/R1_columnIncompatibilities_DPB1.txt + touch results/hla/R1_columnIncompatibilities_DQA1.txt + touch results/hla/R1_columnIncompatibilities_DQB1.txt + touch results/hla/R1_columnIncompatibilities_DRA.txt + touch results/hla/R1_columnIncompatibilities_DRB1.txt + touch results/hla/R1_columnIncompatibilities_DRB3.txt + touch results/hla/R1_columnIncompatibilities_DRB4.txt + touch results/hla/R1_columnIncompatibilities_E.txt + touch results/hla/R1_columnIncompatibilities_F.txt + touch results/hla/R1_columnIncompatibilities_G.txt + touch results/hla/R1_columnIncompatibilities_H.txt + touch results/hla/R1_columnIncompatibilities_K.txt + touch results/hla/R1_columnIncompatibilities_V.txt + touch results/hla/R1_parameters.txt + touch results/hla/R1_pileup_A.txt + touch results/hla/R1_pileup_B.txt + touch results/hla/R1_pileup_C.txt + touch results/hla/R1_pileup_DPA1.txt + touch results/hla/R1_pileup_DPB1.txt + touch results/hla/R1_pileup_DQA1.txt + touch results/hla/R1_pileup_DQB1.txt + touch results/hla/R1_pileup_DRA.txt + touch results/hla/R1_pileup_DRB1.txt + touch results/hla/R1_pileup_DRB3.txt + touch results/hla/R1_pileup_DRB4.txt + touch results/hla/R1_pileup_E.txt + touch results/hla/R1_pileup_F.txt + touch results/hla/R1_pileup_G.txt + touch results/hla/R1_pileup_H.txt + touch results/hla/R1_pileup_K.txt + touch results/hla/R1_pileup_V.txt + touch results/hla/R1_PP_A_pairs.txt + touch results/hla/R1_PP_B_pairs.txt + touch results/hla/R1_PP_C_pairs.txt + touch results/hla/R1_PP_DPA1_pairs.txt + touch results/hla/R1_PP_DPB1_pairs.txt + touch results/hla/R1_PP_DQA1_pairs.txt + touch results/hla/R1_PP_DQB1_pairs.txt + touch results/hla/R1_PP_DRA_pairs.txt + touch results/hla/R1_PP_DRB1_pairs.txt + touch results/hla/R1_PP_DRB3_pairs.txt + touch results/hla/R1_PP_DRB4_pairs.txt + touch results/hla/R1_PP_E_pairs.txt + touch results/hla/R1_PP_F_pairs.txt + touch results/hla/R1_PP_G_pairs.txt + touch results/hla/R1_PP_H_pairs.txt + touch results/hla/R1_PP_K_pairs.txt + touch results/hla/R1_PP_V_pairs.txt + touch results/hla/R1_readIDs_A.txt + touch results/hla/R1_readIDs_B.txt + touch results/hla/R1_readIDs_C.txt + touch results/hla/R1_readIDs_DPA1.txt + touch results/hla/R1_readIDs_DPB1.txt + touch results/hla/R1_readIDs_DQA1.txt + touch results/hla/R1_readIDs_DQB1.txt + touch results/hla/R1_readIDs_DRA.txt + touch results/hla/R1_readIDs_DRB1.txt + touch results/hla/R1_readIDs_DRB3.txt + touch results/hla/R1_readIDs_DRB4.txt + touch results/hla/R1_readIDs_E.txt + touch results/hla/R1_readIDs_F.txt + touch results/hla/R1_readIDs_G.txt + touch results/hla/R1_readIDs_H.txt + touch results/hla/R1_readIDs_K.txt + touch results/hla/R1_readIDs_V.txt + touch results/hla/summaryStatistics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hla-la: ${VERSION} + END_VERSIONS + """ +} diff --git a/modules/nf-core/hlala/typing/meta.yml b/modules/nf-core/hlala/typing/meta.yml new file mode 100644 index 0000000..c5a2cbb --- /dev/null +++ b/modules/nf-core/hlala/typing/meta.yml @@ -0,0 +1,157 @@ +name: "hlala_typing" +description: Performs HLA typing based on a population reference graph and employs + a new linear projection method to align reads to the graph. +keywords: + - hla + - hlala + - hla_typing + - hlala_typing +tools: + - hlala: + description: "HLA typing from short and long reads" + homepage: "https://github.com/DiltheyLab/HLA-LA" + documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala" + tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" + doi: "10.1093/bioinformatics/btz235" + licence: ["GPL"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: [] + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + ontologies: [] + - graph: + type: directory + description: Path to prepared graph with hla-la --action prepareGraph +output: + results: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results: + type: file + description: Results file + ontologies: [] + extraction: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/extraction.bam: + type: file + description: Extraction BAM file + pattern: "*.bam" + ontologies: [] + extraction_index: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/extraction.bam.bai: + type: file + description: Extraction BAM index file + pattern: "*.bam.bai" + ontologies: [] + extraction_mapped: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/extraction_mapped.bam: + type: file + description: Extraction mapped BAM file + pattern: "*.bam" + ontologies: [] + extraction_unmpapped: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/extraction_unmapped.bam: + type: file + description: Extraction unmapped BAM file + pattern: "*.bam" + ontologies: [] + hla: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/hla/*: + type: file + description: HLA results + ontologies: [] + fastq: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/*.fastq: + type: file + description: Fastq file + pattern: "*.fastq" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ + reads_per_level: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/reads_per_level.txt: + type: file + description: Reads per level + pattern: "*.txt" + ontologies: [] + remapped: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/remapped_with_a.bam: + type: file + description: Remapped BAM file + pattern: "*.bam" + ontologies: [] + remapped_index: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/remapped_with_a.bam.bai: + type: file + description: Remapped BAM index file + pattern: "*.bam.bai" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@mapo9" +maintainers: + - "@mapo9" diff --git a/modules/nf-core/hlala/typing/tests/main.nf.test b/modules/nf-core/hlala/typing/tests/main.nf.test new file mode 100644 index 0000000..7037061 --- /dev/null +++ b/modules/nf-core/hlala/typing/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process HLALA_TYPING" + + script "../main.nf" + process "HLALA_TYPING" + tag "modules" + tag "modules_nfcore" + tag "hlala" + tag "hlala/typing" + tag "hlala/preparegraph" + tag "samtools/index" + tag "untar" + + /* + // This test is commented out as it takes a few hours to complete on 10cpus + // Unfortunately no working small datasets are available for the moment for this tool + test("homo_sapiens - cram bai graph") { + setup { + run ("UNTAR") { + script ("../../../untar/main.nf") + process { + """ + input[0] = [ + [ id: 'PRG_test'], + file("http://www.well.ox.ac.uk/downloads/PRG_MHC_GRCh38_withIMGT.tar.gz", checkIfExists: true) + ] + """ + } + } + run ("HLALA_PREPAREGRAPH") { + script ("../../preparegraph/main.nf") + process { + """ + input[0] = UNTAR.out.untar + """ + } + } + run ("SAMTOOLS_INDEX") { + script ("../../../samtools/index/main.nf") + process { + """ + input[0] = [ + [ id: 'test'], + file("https://dl.dropboxusercontent.com/s/xr99u3vqaimk4vo/NA12878.mini.cram", checkIfExists: true) + ] + """ + } + } + } + when { + process { + """ + input[0] = Channel.of([ + [ id: 'test'], + file("https://dl.dropboxusercontent.com/s/xr99u3vqaimk4vo/NA12878.mini.cram", checkIfExists: true) + ]).combine( + SAMTOOLS_INDEX.out.bai.map{ it[1] } + ).combine( + HLALA_PREPAREGRAPH.out.graph.map{ it[1] } + ) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + bam(process.out.extraction[0][1]).getReadsMD5(), + process.out.extraction_index, + bam(process.out.extraction_mapped[0][1]).getReadsMD5(), + bam(process.out.extraction_unmpapped[0][1]).getReadsMD5(), + process.out.hla, + process.out.fastq, + process.out.reads_per_level, + bam(process.out.remapped[0][1]).getReadsMD5(), + process.out.remapped_index + ).match() } + ) + } + } + */ + + test("homo_sapiens - cram bai graph -- stub") { + options '-stub' + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ]) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml + ).match() } + ) + } + } +} diff --git a/modules/nf-core/hlala/typing/tests/main.nf.test.snap b/modules/nf-core/hlala/typing/tests/main.nf.test.snap new file mode 100644 index 0000000..20156ae --- /dev/null +++ b/modules/nf-core/hlala/typing/tests/main.nf.test.snap @@ -0,0 +1,646 @@ +{ + "homo_sapiens - cram bai graph": { + "content": [ + [ + "versions.yml:md5,15a7d7b635ae0a3e3d5805b7aa00594e" + ], + "4896d6f9116ae911d0ca0b9470f494c3", + [ + [ + { + "id": "test" + }, + "extraction.bam.bai:md5,052a964cdc38cabdd899b0c18ffda7c1" + ] + ], + "a1133c123cfa78df2d1e334de5a55015", + "97de6160bc47d8178aea1eacd1d4cc02", + [ + [ + { + "id": "test" + }, + [ + "R1_PP_A_pairs.txt:md5,028d6b967e67a33e5ca9f4278ff84529", + "R1_PP_B_pairs.txt:md5,8547d792e6f967cbbdd0f246d3ed76a0", + "R1_PP_C_pairs.txt:md5,b5c500284f97ac5b478de687a61b6fad", + "R1_PP_DPA1_pairs.txt:md5,7861ef796ac5e26a6f591f87bd7b12bb", + "R1_PP_DPB1_pairs.txt:md5,218dd810b53b97bc16a6eed62c441eeb", + "R1_PP_DQA1_pairs.txt:md5,393c20e54fe8f612079b8cb16286e45b", + "R1_PP_DQB1_pairs.txt:md5,182d33538312cfdfc5f555fa3f9c4063", + "R1_PP_DRA_pairs.txt:md5,60eec214cac4f74fe2d9910bdeb392dd", + "R1_PP_DRB1_pairs.txt:md5,250323162d4f2bde007eae297337aea4", + "R1_PP_DRB3_pairs.txt:md5,d42a15c6edd8aece48a81e7840871984", + "R1_PP_DRB4_pairs.txt:md5,41020a544ff7b033beaec9634c30705a", + "R1_PP_E_pairs.txt:md5,1fa1555add592bbdbbd237ea66943bfe", + "R1_PP_F_pairs.txt:md5,577702e182398f6a27b956c201e0e1fe", + "R1_PP_G_pairs.txt:md5,1ab4cf022a405a9c212c03feaf2794d2", + "R1_PP_H_pairs.txt:md5,a569fca89956471985b78c7f9227ef3e", + "R1_PP_K_pairs.txt:md5,2ad0d4a08aea44d658f270e9f9567b75", + "R1_PP_V_pairs.txt:md5,abe2b04e46d514fe005ef577271dc3cc", + "R1_bestguess.txt:md5,42a1953376ea13d060e0d1ffafb1a680", + "R1_bestguess_G.txt:md5,cbf2995855ce1603eb56126156e29d1e", + "R1_columnIncompatibilities_A.txt:md5,be5105cb8ae3d0aa0b1e9013e6f68f82", + "R1_columnIncompatibilities_B.txt:md5,fd0cb44777f50b078cfa568a8d7ae345", + "R1_columnIncompatibilities_C.txt:md5,c38c180a9cd8e48be3db0f9945e38195", + "R1_columnIncompatibilities_DPA1.txt:md5,d1421647ceba96c81c2e4529dc41118a", + "R1_columnIncompatibilities_DPB1.txt:md5,4c7c013602f0602120202dace722eaaa", + "R1_columnIncompatibilities_DQA1.txt:md5,71554f91ff04abfb6700ffb9862206bf", + "R1_columnIncompatibilities_DQB1.txt:md5,b42034342785683ccfd71cb58fab8b79", + "R1_columnIncompatibilities_DRA.txt:md5,146bc2a093a4537bf3ad4f417fb430bc", + "R1_columnIncompatibilities_DRB1.txt:md5,890ea396b73a28ae6b1a380ea8bf7fc8", + "R1_columnIncompatibilities_DRB3.txt:md5,9b39dcae8ea002101b2b0cdec4282bd1", + "R1_columnIncompatibilities_DRB4.txt:md5,c8cbbb9af9fdea670b8055d1d93a7b06", + "R1_columnIncompatibilities_E.txt:md5,94d5b4b982c97165a7d428e5d07ad3cd", + "R1_columnIncompatibilities_F.txt:md5,0425a4304c94a9e468a59bafeeabdcd4", + 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"R1_pileup_DRB4.txt:md5,cc19d8e8774a92fbbb0dd45bdb60f625", + "R1_pileup_E.txt:md5,fbd1dfd0be412505f1eb95aa4fc06586", + "R1_pileup_F.txt:md5,b0ecac311c70b3b37434c80125913b7a", + "R1_pileup_G.txt:md5,e0a65200a51e2b40737dee8873704302", + "R1_pileup_H.txt:md5,307644c4f412265a88398de0135208e2", + "R1_pileup_K.txt:md5,84f608d3175cc093e80b0f68b51d90c2", + "R1_pileup_V.txt:md5,e1308b2721e81d46e8277a5da2b6c4f2", + "R1_readIDs_A.txt:md5,bcc2546cc5d69337d3964a0750c04727", + "R1_readIDs_B.txt:md5,df01e6d2c1c9094597d293fc2be2ffcf", + "R1_readIDs_C.txt:md5,a48640796d369422bf192389ad86e464", + "R1_readIDs_DPA1.txt:md5,30e4496305c3df915c9da5a5f24b7900", + "R1_readIDs_DPB1.txt:md5,3e3079ac361e5183e1d23ed94373e5b1", + "R1_readIDs_DQA1.txt:md5,1bb2b34757d6968043b15c7654a9ce65", + "R1_readIDs_DQB1.txt:md5,082151c0f1b0b0eb5e7a3510e7e35be7", + "R1_readIDs_DRA.txt:md5,d608075cde7e9ea3cd4fe79706d0a6fc", + "R1_readIDs_DRB1.txt:md5,71e62e469c0428cf41a73baefd4e8286", + 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"R1_PP_G_pairs.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_PP_H_pairs.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_PP_K_pairs.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_PP_V_pairs.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_bestguess.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_bestguess_G.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_A.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_B.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_C.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DPA1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DPB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DQA1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DQB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DRA.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DRB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DRB3.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_DRB4.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_E.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_F.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_G.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_H.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_K.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_columnIncompatibilities_V.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_parameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_A.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_B.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_C.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DPA1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DPB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DQA1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DQB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DRA.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DRB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DRB3.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_DRB4.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_E.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_F.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_G.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_H.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_K.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_pileup_V.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_A.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_B.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_C.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DPA1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DPB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DQA1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DQB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DRA.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DRB1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DRB3.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_DRB4.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_E.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_F.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_G.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_H.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_K.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "R1_readIDs_V.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "histogram_matchesPerRead.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "summaryStatistics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "reads_per_level.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "remapped_with_a.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "remapped_with_a.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,15a7d7b635ae0a3e3d5805b7aa00594e" + ] + }, + { + "HLALA_TYPING": { + "hla-la": "1.0.4" + } + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-15T16:04:37.27101156" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 068865c..7d8bff0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,12 +20,16 @@ params { // Alignment save_merged_fastq = false - // HLA typing tools to run (comma-separated list, valid options: 'optitype', 'hlahd') + // HLA typing tools to run (comma-separated list, valid options: 'optitype', 'hlahd', 'hlala') tools = 'optitype' // Set the HLA-HD installation tarball hlahd_path = null // Should the HLA-HD reference dictionary be updated to the latest version from the IGMT/HLA database? hlahd_update_reference_dict = false + // Path to HLA*LA graph tarball (optional, will be downloaded if not provided) + hlala_graph_tarball = null + // Path to pre-built HLA*LA graph parent directory (optional, skips download if provided) + hlala_graph_dir = null // References genome = null @@ -190,6 +194,8 @@ profiles { test_dna_rna { includeConfig 'conf/test_dna_rna.config' } test_hlahd { includeConfig 'conf/test_hlahd.config' } test_optitype_hlahd { includeConfig 'conf/test_optitype_hlahd.config' } + test_hlala { includeConfig 'conf/test_hlala.config' } + test_optitype_hlala { includeConfig 'conf/test_optitype_hlala.config' } } // Load nf-core custom profiles from different institutions diff --git a/nextflow_schema.json b/nextflow_schema.json index 5a23ebc..15ffe8f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -47,7 +47,7 @@ "tools": { "type": "string", "default": "optitype", - "help_text": "Specifies the tool(s) to use. Multiple tools can be combined in a list separated by comma.\nAvailable are: `optitype`, `hlahd`.", + "help_text": "Specifies the tool(s) to use. Multiple tools can be combined in a list separated by comma.\nAvailable are: `optitype`, `hlahd`, `hlala`.", "description": "Specifies the hlatyping tool(s) to use." } } @@ -110,6 +110,30 @@ } } }, + "hlala_options": { + "title": "HLA*LA options", + "type": "object", + "description": "Options for running HLA*LA for HLA typing from BAM files.", + "default": "", + "fa_icon": "fas fa-dna", + "properties": { + "hlala_graph_tarball": { + "type": "string", + "default": null, + "fa_icon": "fas fa-file-archive", + "description": "Path to HLA*LA graph tarball (optional).", + "help_text": "Path to the HLA*LA graph tarball (PRG_MHC_GRCh38_withIMGT.tar.gz). If provided, it will be validated and extracted. If not provided, the graph will be downloaded automatically from Oxford servers." + }, + "hlala_graph_dir": { + "type": "string", + "default": null, + "format": "directory-path", + "fa_icon": "fas fa-folder-open", + "description": "Path to pre-built HLA*LA graph parent directory (optional).", + "help_text": "Path to the parent directory containing the HLA*LA graph (e.g., the directory that contains `PRG_MHC_GRCh38_withIMGT/`). If provided, skips graph download entirely. Takes precedence over `hlala_graph_tarball`." + } + } + }, "reference_genome_options": { "title": "Reference genome options", "type": "object", @@ -323,6 +347,9 @@ { "$ref": "#/$defs/hlahd_options" }, + { + "$ref": "#/$defs/hlala_options" + }, { "$ref": "#/$defs/reference_genome_options" }, diff --git a/subworkflows/local/utils_nfcore_hlatyping_pipeline/main.nf b/subworkflows/local/utils_nfcore_hlatyping_pipeline/main.nf index 76a5b9c..b21e0b6 100644 --- a/subworkflows/local/utils_nfcore_hlatyping_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_hlatyping_pipeline/main.nf @@ -198,7 +198,7 @@ def validateInputParameters() { // def validateToolsParam() { def tools = params.tools ?: 'optitype' - def valid_tools = [ 'optitype', 'hlahd' ] + def valid_tools = [ 'optitype', 'hlahd', 'hlala' ] def tool_list = tools.tokenize(',') def invalid_tools = tool_list.findAll { tool -> tool.trim() !in valid_tools } if (invalid_tools) { diff --git a/tests/.nftignore b/tests/.nftignore index 76f45b0..cbab90b 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -9,5 +9,6 @@ multiqc/multiqc_report.html fastqc/*_fastqc.{html,zip} optitype/**/* hlahd/**/*.{bam,bai,pdf,tsv} +hlala/**/* yara/**/*.{bam,bai} pipeline_info/*.{html,json,txt,yml} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f0ffaa7..fdc2e32 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -27,9 +27,6 @@ } }, [ - "check", - "check/example_pe.bam", - "check/is_singleend.txt", "fastqc", "fastqc/SAMPLE_PAIRED_END_BAM_1_fastqc.html", "fastqc/SAMPLE_PAIRED_END_BAM_1_fastqc.zip", @@ -97,58 +94,16 @@ "optitype/SAMPLE_PAIRED_END_BAM/SAMPLE_PAIRED_END_BAM_coverage_plot.pdf", "optitype/SAMPLE_PAIRED_END_BAM/SAMPLE_PAIRED_END_BAM_result.tsv", "pipeline_info", - "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml", - "samtools", - "samtools/SAMPLE_PAIRED_END_BAM_1.fq.gz", - "samtools/SAMPLE_PAIRED_END_BAM_2.fq.gz", - "samtools/SAMPLE_PAIRED_END_BAM_other.fq.gz", - "samtools/SAMPLE_PAIRED_END_BAM_singleton.fq.gz", - "yara", - "yara/SAMPLE_PAIRED_END_BAM", - "yara/SAMPLE_PAIRED_END_BAM/SAMPLE_PAIRED_END_BAM_1.mapped.bam", - "yara/SAMPLE_PAIRED_END_BAM/SAMPLE_PAIRED_END_BAM_1.mapped.bam.bai", - "yara/SAMPLE_PAIRED_END_BAM/SAMPLE_PAIRED_END_BAM_2.mapped.bam", - "yara/SAMPLE_PAIRED_END_BAM/SAMPLE_PAIRED_END_BAM_2.mapped.bam.bai", - "yara/SAMPLE_PAIRED_END_BAM/versions.yml", - "yara/hla_reference_dna.fasta.lf.drp", - "yara/hla_reference_dna.fasta.lf.drs", - "yara/hla_reference_dna.fasta.lf.drv", - "yara/hla_reference_dna.fasta.lf.pst", - "yara/hla_reference_dna.fasta.rid.concat", - "yara/hla_reference_dna.fasta.rid.limits", - "yara/hla_reference_dna.fasta.sa.ind", - "yara/hla_reference_dna.fasta.sa.len", - "yara/hla_reference_dna.fasta.sa.val", - "yara/hla_reference_dna.fasta.txt.concat", - "yara/hla_reference_dna.fasta.txt.limits", - "yara/hla_reference_dna.fasta.txt.size" + "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml" ], [ - "example_pe.bam:md5,e6145c17fef62ea071238f8b0aca841c", - "is_singleend.txt:md5,d42f2da1df5ecdf29be4ac27edda0c12", - "SAMPLE_PAIRED_END_BAM_1.fq.gz:md5,361598a72f419e19c4de108267fa330c", - "SAMPLE_PAIRED_END_BAM_2.fq.gz:md5,45854c8203e7b26e0e2904c2f2dd6d3f", - "SAMPLE_PAIRED_END_BAM_other.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "SAMPLE_PAIRED_END_BAM_singleton.fq.gz:md5,fc978e9e59035f8f1739edf71c648796", - "versions.yml:md5,3d67d5a34bf0044c6567763154ac1719", - "hla_reference_dna.fasta.lf.drp:md5,28d863bdb814bccb8212a7b451e2af0a", - "hla_reference_dna.fasta.lf.drs:md5,8666683506aacd900bbd5a74ac4edf68", - "hla_reference_dna.fasta.lf.drv:md5,98fa3e81b21cb85d1c9a7d701a831f0e", - "hla_reference_dna.fasta.lf.pst:md5,7e4fafea7f4d82c0407316c624c91000", - "hla_reference_dna.fasta.rid.concat:md5,d9a10cb0542c3d2b11b9f7ecc81cee1b", - "hla_reference_dna.fasta.rid.limits:md5,167fc45e03c303ff240e0815511e3035", - "hla_reference_dna.fasta.sa.ind:md5,f12fbb7fb0cca69fd5a6a38dbe1c6f7a", - "hla_reference_dna.fasta.sa.len:md5,4649b6c24c69d4658c983376459d6e9e", - "hla_reference_dna.fasta.sa.val:md5,a04df027b40bb0aa08dd61a765a79c02", - "hla_reference_dna.fasta.txt.concat:md5,d9da1795da878cdaacf5e41d88732edf", - "hla_reference_dna.fasta.txt.limits:md5,e84e544db01cc5090be2857f765a3f80", - "hla_reference_dna.fasta.txt.size:md5,704808ea26959edde70643c8e44afeb0" + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-30T13:17:45.420883473" + "timestamp": "2026-02-27T10:34:35.022499763" } } \ No newline at end of file diff --git a/tests/dna_rna.nf.test.snap b/tests/dna_rna.nf.test.snap index 0166b64..bbb6dcc 100644 --- a/tests/dna_rna.nf.test.snap +++ b/tests/dna_rna.nf.test.snap @@ -103,78 +103,16 @@ "optitype/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_coverage_plot.pdf", "optitype/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_result.tsv", "pipeline_info", - "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml", - "yara", - "yara/SAMPLE_FASTQ", - "yara/SAMPLE_FASTQ/SAMPLE_FASTQ_1.mapped.bam", - "yara/SAMPLE_FASTQ/SAMPLE_FASTQ_1.mapped.bam.bai", - "yara/SAMPLE_FASTQ/SAMPLE_FASTQ_2.mapped.bam", - "yara/SAMPLE_FASTQ/SAMPLE_FASTQ_2.mapped.bam.bai", - "yara/SAMPLE_FASTQ/versions.yml", - "yara/SAMPLE_FASTQ_RNA", - "yara/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_1.mapped.bam", - "yara/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_1.mapped.bam.bai", - "yara/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_2.mapped.bam", - "yara/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_2.mapped.bam.bai", - "yara/SAMPLE_FASTQ_RNA/versions.yml", - "yara/hla_reference_dna.fasta.lf.drp", - "yara/hla_reference_dna.fasta.lf.drs", - "yara/hla_reference_dna.fasta.lf.drv", - "yara/hla_reference_dna.fasta.lf.pst", - "yara/hla_reference_dna.fasta.rid.concat", - "yara/hla_reference_dna.fasta.rid.limits", - "yara/hla_reference_dna.fasta.sa.ind", - "yara/hla_reference_dna.fasta.sa.len", - "yara/hla_reference_dna.fasta.sa.val", - "yara/hla_reference_dna.fasta.txt.concat", - "yara/hla_reference_dna.fasta.txt.limits", - "yara/hla_reference_dna.fasta.txt.size", - "yara/hla_reference_rna.fasta.lf.drp", - "yara/hla_reference_rna.fasta.lf.drs", - "yara/hla_reference_rna.fasta.lf.drv", - "yara/hla_reference_rna.fasta.lf.pst", - "yara/hla_reference_rna.fasta.rid.concat", - "yara/hla_reference_rna.fasta.rid.limits", - "yara/hla_reference_rna.fasta.sa.ind", - "yara/hla_reference_rna.fasta.sa.len", - "yara/hla_reference_rna.fasta.sa.val", - "yara/hla_reference_rna.fasta.txt.concat", - "yara/hla_reference_rna.fasta.txt.limits", - "yara/hla_reference_rna.fasta.txt.size" + "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml" ], [ - "versions.yml:md5,3d67d5a34bf0044c6567763154ac1719", - "versions.yml:md5,3d67d5a34bf0044c6567763154ac1719", - "hla_reference_dna.fasta.lf.drp:md5,28d863bdb814bccb8212a7b451e2af0a", - "hla_reference_dna.fasta.lf.drs:md5,8666683506aacd900bbd5a74ac4edf68", - "hla_reference_dna.fasta.lf.drv:md5,98fa3e81b21cb85d1c9a7d701a831f0e", - "hla_reference_dna.fasta.lf.pst:md5,7e4fafea7f4d82c0407316c624c91000", - "hla_reference_dna.fasta.rid.concat:md5,d9a10cb0542c3d2b11b9f7ecc81cee1b", - "hla_reference_dna.fasta.rid.limits:md5,167fc45e03c303ff240e0815511e3035", - "hla_reference_dna.fasta.sa.ind:md5,f12fbb7fb0cca69fd5a6a38dbe1c6f7a", - "hla_reference_dna.fasta.sa.len:md5,4649b6c24c69d4658c983376459d6e9e", - "hla_reference_dna.fasta.sa.val:md5,a04df027b40bb0aa08dd61a765a79c02", - "hla_reference_dna.fasta.txt.concat:md5,d9da1795da878cdaacf5e41d88732edf", - "hla_reference_dna.fasta.txt.limits:md5,e84e544db01cc5090be2857f765a3f80", - "hla_reference_dna.fasta.txt.size:md5,704808ea26959edde70643c8e44afeb0", - "hla_reference_rna.fasta.lf.drp:md5,128d936b51ae31a29180daafcfcdd268", - "hla_reference_rna.fasta.lf.drs:md5,8666683506aacd900bbd5a74ac4edf68", - "hla_reference_rna.fasta.lf.drv:md5,2b70a39065cb4cebcb61c4fbe58ed80d", - "hla_reference_rna.fasta.lf.pst:md5,c4953215c2d6ca2d0778f7beac6cb112", - "hla_reference_rna.fasta.rid.concat:md5,265a1473f4582251df3a7e8cfac2c9d4", - "hla_reference_rna.fasta.rid.limits:md5,fccc5296404a012cfd5f4b99242250db", - "hla_reference_rna.fasta.sa.ind:md5,7a8a7f1ca8fbe7ee5409cf0a0337ad9c", - "hla_reference_rna.fasta.sa.len:md5,a9b77a9d99a950a3e8ac16709144c6db", - "hla_reference_rna.fasta.sa.val:md5,2aff12256a8f936264d0d843ccd2fd97", - "hla_reference_rna.fasta.txt.concat:md5,d3975911cdc2d224763528f1a08773fe", - "hla_reference_rna.fasta.txt.limits:md5,6be3fe29235eac6f36ecee28eba11697", - "hla_reference_rna.fasta.txt.size:md5,5b932358d7f42f3a5b52a4e567020d85" + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-30T13:23:11.844176962" + "timestamp": "2026-02-27T10:54:41.193715344" } } \ No newline at end of file diff --git a/tests/fastq.nf.test.snap b/tests/fastq.nf.test.snap index 221f578..66ce184 100644 --- a/tests/fastq.nf.test.snap +++ b/tests/fastq.nf.test.snap @@ -88,47 +88,16 @@ "optitype/SAMPLE_PAIRED_END/SAMPLE_PAIRED_END_coverage_plot.pdf", "optitype/SAMPLE_PAIRED_END/SAMPLE_PAIRED_END_result.tsv", "pipeline_info", - "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml", - "yara", - "yara/SAMPLE_PAIRED_END", - "yara/SAMPLE_PAIRED_END/SAMPLE_PAIRED_END_1.mapped.bam", - "yara/SAMPLE_PAIRED_END/SAMPLE_PAIRED_END_1.mapped.bam.bai", - "yara/SAMPLE_PAIRED_END/SAMPLE_PAIRED_END_2.mapped.bam", - "yara/SAMPLE_PAIRED_END/SAMPLE_PAIRED_END_2.mapped.bam.bai", - "yara/SAMPLE_PAIRED_END/versions.yml", - "yara/hla_reference_dna.fasta.lf.drp", - "yara/hla_reference_dna.fasta.lf.drs", - "yara/hla_reference_dna.fasta.lf.drv", - "yara/hla_reference_dna.fasta.lf.pst", - "yara/hla_reference_dna.fasta.rid.concat", - "yara/hla_reference_dna.fasta.rid.limits", - "yara/hla_reference_dna.fasta.sa.ind", - "yara/hla_reference_dna.fasta.sa.len", - "yara/hla_reference_dna.fasta.sa.val", - "yara/hla_reference_dna.fasta.txt.concat", - "yara/hla_reference_dna.fasta.txt.limits", - "yara/hla_reference_dna.fasta.txt.size" + "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml" ], [ - "versions.yml:md5,3d67d5a34bf0044c6567763154ac1719", - "hla_reference_dna.fasta.lf.drp:md5,28d863bdb814bccb8212a7b451e2af0a", - "hla_reference_dna.fasta.lf.drs:md5,8666683506aacd900bbd5a74ac4edf68", - "hla_reference_dna.fasta.lf.drv:md5,98fa3e81b21cb85d1c9a7d701a831f0e", - "hla_reference_dna.fasta.lf.pst:md5,7e4fafea7f4d82c0407316c624c91000", - "hla_reference_dna.fasta.rid.concat:md5,d9a10cb0542c3d2b11b9f7ecc81cee1b", - "hla_reference_dna.fasta.rid.limits:md5,167fc45e03c303ff240e0815511e3035", - "hla_reference_dna.fasta.sa.ind:md5,f12fbb7fb0cca69fd5a6a38dbe1c6f7a", - "hla_reference_dna.fasta.sa.len:md5,4649b6c24c69d4658c983376459d6e9e", - "hla_reference_dna.fasta.sa.val:md5,a04df027b40bb0aa08dd61a765a79c02", - "hla_reference_dna.fasta.txt.concat:md5,d9da1795da878cdaacf5e41d88732edf", - "hla_reference_dna.fasta.txt.limits:md5,e84e544db01cc5090be2857f765a3f80", - "hla_reference_dna.fasta.txt.size:md5,704808ea26959edde70643c8e44afeb0" + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-30T13:28:12.89751644" + "timestamp": "2026-02-27T10:54:22.834194425" } } \ No newline at end of file diff --git a/tests/fastq_cat.nf.test.snap b/tests/fastq_cat.nf.test.snap index 5eb1b36..64658f1 100644 --- a/tests/fastq_cat.nf.test.snap +++ b/tests/fastq_cat.nf.test.snap @@ -106,78 +106,16 @@ "optitype/SAMPLE_FASTQ_RNA_CAT/SAMPLE_FASTQ_RNA_CAT_coverage_plot.pdf", "optitype/SAMPLE_FASTQ_RNA_CAT/SAMPLE_FASTQ_RNA_CAT_result.tsv", "pipeline_info", - "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml", - "yara", - "yara/SAMPLE_FASTQ_CAT", - "yara/SAMPLE_FASTQ_CAT/SAMPLE_FASTQ_CAT_1.mapped.bam", - "yara/SAMPLE_FASTQ_CAT/SAMPLE_FASTQ_CAT_1.mapped.bam.bai", - "yara/SAMPLE_FASTQ_CAT/SAMPLE_FASTQ_CAT_2.mapped.bam", - "yara/SAMPLE_FASTQ_CAT/SAMPLE_FASTQ_CAT_2.mapped.bam.bai", - "yara/SAMPLE_FASTQ_CAT/versions.yml", - "yara/SAMPLE_FASTQ_RNA_CAT", - "yara/SAMPLE_FASTQ_RNA_CAT/SAMPLE_FASTQ_RNA_CAT_1.mapped.bam", - "yara/SAMPLE_FASTQ_RNA_CAT/SAMPLE_FASTQ_RNA_CAT_1.mapped.bam.bai", - "yara/SAMPLE_FASTQ_RNA_CAT/SAMPLE_FASTQ_RNA_CAT_2.mapped.bam", - "yara/SAMPLE_FASTQ_RNA_CAT/SAMPLE_FASTQ_RNA_CAT_2.mapped.bam.bai", - "yara/SAMPLE_FASTQ_RNA_CAT/versions.yml", - "yara/hla_reference_dna.fasta.lf.drp", - "yara/hla_reference_dna.fasta.lf.drs", - "yara/hla_reference_dna.fasta.lf.drv", - "yara/hla_reference_dna.fasta.lf.pst", - "yara/hla_reference_dna.fasta.rid.concat", - "yara/hla_reference_dna.fasta.rid.limits", - "yara/hla_reference_dna.fasta.sa.ind", - "yara/hla_reference_dna.fasta.sa.len", - "yara/hla_reference_dna.fasta.sa.val", - "yara/hla_reference_dna.fasta.txt.concat", - "yara/hla_reference_dna.fasta.txt.limits", - "yara/hla_reference_dna.fasta.txt.size", - "yara/hla_reference_rna.fasta.lf.drp", - "yara/hla_reference_rna.fasta.lf.drs", - "yara/hla_reference_rna.fasta.lf.drv", - "yara/hla_reference_rna.fasta.lf.pst", - "yara/hla_reference_rna.fasta.rid.concat", - "yara/hla_reference_rna.fasta.rid.limits", - "yara/hla_reference_rna.fasta.sa.ind", - "yara/hla_reference_rna.fasta.sa.len", - "yara/hla_reference_rna.fasta.sa.val", - "yara/hla_reference_rna.fasta.txt.concat", - "yara/hla_reference_rna.fasta.txt.limits", - "yara/hla_reference_rna.fasta.txt.size" + "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml" ], [ - "versions.yml:md5,3d67d5a34bf0044c6567763154ac1719", - "versions.yml:md5,3d67d5a34bf0044c6567763154ac1719", - "hla_reference_dna.fasta.lf.drp:md5,28d863bdb814bccb8212a7b451e2af0a", - "hla_reference_dna.fasta.lf.drs:md5,8666683506aacd900bbd5a74ac4edf68", - "hla_reference_dna.fasta.lf.drv:md5,98fa3e81b21cb85d1c9a7d701a831f0e", - "hla_reference_dna.fasta.lf.pst:md5,7e4fafea7f4d82c0407316c624c91000", - "hla_reference_dna.fasta.rid.concat:md5,d9a10cb0542c3d2b11b9f7ecc81cee1b", - "hla_reference_dna.fasta.rid.limits:md5,167fc45e03c303ff240e0815511e3035", - "hla_reference_dna.fasta.sa.ind:md5,f12fbb7fb0cca69fd5a6a38dbe1c6f7a", - "hla_reference_dna.fasta.sa.len:md5,4649b6c24c69d4658c983376459d6e9e", - "hla_reference_dna.fasta.sa.val:md5,a04df027b40bb0aa08dd61a765a79c02", - "hla_reference_dna.fasta.txt.concat:md5,d9da1795da878cdaacf5e41d88732edf", - "hla_reference_dna.fasta.txt.limits:md5,e84e544db01cc5090be2857f765a3f80", - "hla_reference_dna.fasta.txt.size:md5,704808ea26959edde70643c8e44afeb0", - "hla_reference_rna.fasta.lf.drp:md5,128d936b51ae31a29180daafcfcdd268", - "hla_reference_rna.fasta.lf.drs:md5,8666683506aacd900bbd5a74ac4edf68", - "hla_reference_rna.fasta.lf.drv:md5,2b70a39065cb4cebcb61c4fbe58ed80d", - "hla_reference_rna.fasta.lf.pst:md5,c4953215c2d6ca2d0778f7beac6cb112", - "hla_reference_rna.fasta.rid.concat:md5,265a1473f4582251df3a7e8cfac2c9d4", - "hla_reference_rna.fasta.rid.limits:md5,fccc5296404a012cfd5f4b99242250db", - "hla_reference_rna.fasta.sa.ind:md5,7a8a7f1ca8fbe7ee5409cf0a0337ad9c", - "hla_reference_rna.fasta.sa.len:md5,a9b77a9d99a950a3e8ac16709144c6db", - "hla_reference_rna.fasta.sa.val:md5,2aff12256a8f936264d0d843ccd2fd97", - "hla_reference_rna.fasta.txt.concat:md5,d3975911cdc2d224763528f1a08773fe", - "hla_reference_rna.fasta.txt.limits:md5,6be3fe29235eac6f36ecee28eba11697", - "hla_reference_rna.fasta.txt.size:md5,5b932358d7f42f3a5b52a4e567020d85" + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-30T13:34:00.224201861" + "timestamp": "2026-02-27T10:54:53.828956144" } } \ No newline at end of file diff --git a/tests/hlahd.nf.test.snap b/tests/hlahd.nf.test.snap index b96d7d7..2789071 100644 --- a/tests/hlahd.nf.test.snap +++ b/tests/hlahd.nf.test.snap @@ -28,687 +28,6 @@ "hlahd/SAMPLE_FASTQ/SAMPLE_FASTQ_final.result.txt", "hlahd/SAMPLE_FASTQ_RNA", "hlahd/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_final.result.txt", - "hlahd/hlahd", - "hlahd/hlahd/1.7.1", - "hlahd/hlahd/1.7.1/._HLA_gene.split.3.32.0.txt", - "hlahd/hlahd/1.7.1/HLA_gene.split.3.32.0.txt", - "hlahd/hlahd/1.7.1/HLA_gene.split.3.50.0.txt", - "hlahd/hlahd/1.7.1/HLA_gene.split.txt", - "hlahd/hlahd/1.7.1/Readme.txt", - "hlahd/hlahd/1.7.1/bin", - "hlahd/hlahd/1.7.1/bin/drop_intron_map", - "hlahd/hlahd/1.7.1/bin/get_diff_fasta", - "hlahd/hlahd/1.7.1/bin/hla_est", - "hlahd/hlahd/1.7.1/bin/hlahd.1.6.1.sh", - "hlahd/hlahd/1.7.1/bin/hlahd.sh", - "hlahd/hlahd/1.7.1/bin/pick_up_allele", - "hlahd/hlahd/1.7.1/bin/pm_extract", - "hlahd/hlahd/1.7.1/bin/split_pm_read", - "hlahd/hlahd/1.7.1/bin/split_shell", - "hlahd/hlahd/1.7.1/bin/stfr", - "hlahd/hlahd/1.7.1/data", - "hlahd/hlahd/1.7.1/dictionary", - "hlahd/hlahd/1.7.1/dictionary/A", - "hlahd/hlahd/1.7.1/dictionary/A/A.list", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon1_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon2_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon3_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon4_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon5_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon6_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon7_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_exon8_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_gen_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_gen_w_utr_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_intron1_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_intron2_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_intron3_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_intron4_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_intron5_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_intron6_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_intron7_N150.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_utr3.fasta", - "hlahd/hlahd/1.7.1/dictionary/A/A_utr5.fasta", - "hlahd/hlahd/1.7.1/dictionary/B", - "hlahd/hlahd/1.7.1/dictionary/B/B.list", - 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- "Reselect.h:md5,6253152f9494bc10319c53d48794f917", - "STFR_Tools.h:md5,25b963aa5668c0c5b03d82a993b34d71", - "STFR_define.h:md5,693746eda2581c756a02c34373a913a4", - "Select.h:md5,0fdd5dcb83a651413744a44f49cbdf88", - "Sort.h:md5,86525133c3283db923a57b3c85e255a5", - "Tools.h:md5,fe31f954bf64faec004f5fbe7dd8acde", - "Tree.h:md5,40ca19ef9c3e6f6a1329dcdbbd4c23d1", - "drop_intron_map.cpp:md5,135a5cfc79db39a12918a65090fec863", - "get_diff_fasta.cpp:md5,e5ef4356f302a78defad40cd24bf0e12", - "hla_estimation.cpp:md5,3ddf326dd1daf338ace98badaf492f58", - "pick_up_allele.cpp:md5,594d7a06d14ccac0528eae2653945c41", - "pm_extract.cpp:md5,d35b4a218ae3c4a1ddd496d65afe46bd", - "sam_to_fastq_reverse.cpp:md5,03dab4ce8a127405be3009f763086976", - "split_PM_reads.cpp:md5,5b50d52dd1a2e1c525f47cc2d670f6ec", - "split_shell.cpp:md5,9ecf85870bff57eb22d04a50b11be2bc", - "update.dictionary.sh:md5,f885ef234cc3999f18d80b93d78d8b40" + "SAMPLE_FASTQ_RNA_final.result.txt:md5,15e8f8fe058169c02f4136e092981500" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-30T12:17:55.040437773" + "timestamp": "2026-02-27T11:36:22.421062456" } } \ No newline at end of file diff --git a/tests/hlala.nf.test b/tests/hlala.nf.test new file mode 100644 index 0000000..fe47c8d --- /dev/null +++ b/tests/hlala.nf.test @@ -0,0 +1,37 @@ +nextflow_pipeline { + + name "Test pipeline with HLA*LA" + script "../main.nf" + tag "hlala" + profile "test_hlala" + options "-stub-run" + + test("-profile test_hlala (stub)") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_hlatyping_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/hlala.nf.test.snap b/tests/hlala.nf.test.snap new file mode 100644 index 0000000..36f4a93 --- /dev/null +++ b/tests/hlala.nf.test.snap @@ -0,0 +1,137 @@ +{ + "-profile test_hlala (stub)": { + "content": [ + 7, + { + "CHECK_PAIRED": { + "samtools": "1.16.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "HLALA_DOWNLOAD": { + "wget": "1.21.4" + }, + "HLALA_TYPING": { + "hla-la": "1.0.4" + }, + "SAMTOOLS_COLLATEFASTQ": { + "samtools": 1.21 + }, + "SAMTOOLS_VIEW": { + "samtools": 1.21 + }, + "Workflow": { + "nf-core/hlatyping": "v2.2.0" + } + }, + [ + "fastqc", + "fastqc/SAMPLE_PAIRED_END_BAM.html", + "fastqc/SAMPLE_PAIRED_END_BAM.zip", + "hlala", + "hlala/SAMPLE_PAIRED_END_BAM", + "hlala/SAMPLE_PAIRED_END_BAM/results", + "hlala/SAMPLE_PAIRED_END_BAM/results/R_1.fastq", + "hlala/SAMPLE_PAIRED_END_BAM/results/R_2.fastq", + "hlala/SAMPLE_PAIRED_END_BAM/results/R_U.fastq", + "hlala/SAMPLE_PAIRED_END_BAM/results/extraction.bam", + "hlala/SAMPLE_PAIRED_END_BAM/results/extraction.bam.bai", + "hlala/SAMPLE_PAIRED_END_BAM/results/extraction_mapped.bam", + "hlala/SAMPLE_PAIRED_END_BAM/results/extraction_unmapped.bam", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_A_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_B_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_C_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DPA1_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DPB1_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DQA1_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DQB1_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DRA_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DRB1_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DRB3_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_DRB4_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_E_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_F_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_G_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_H_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_K_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_PP_V_pairs.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_bestguess.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_bestguess_G.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_A.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_B.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_C.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DPA1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DPB1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DQA1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DQB1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DRA.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DRB1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DRB3.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_DRB4.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_E.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_F.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_G.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_H.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_K.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_columnIncompatibilities_V.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_parameters.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_A.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_B.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_C.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DPA1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DPB1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DQA1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DQB1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DRA.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DRB1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DRB3.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_DRB4.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_E.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_F.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_G.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_H.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_K.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_pileup_V.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_readIDs_A.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_readIDs_B.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_readIDs_C.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_readIDs_DPA1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_readIDs_DPB1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_readIDs_DQA1.txt", + "hlala/SAMPLE_PAIRED_END_BAM/results/hla/R1_readIDs_DQB1.txt", + 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"multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml" + ], + [ + "SAMPLE_PAIRED_END_BAM.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAMPLE_PAIRED_END_BAM.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-27T10:37:40.952629022" + } +} \ No newline at end of file diff --git a/tests/optitype_hlahd.nf.test.snap b/tests/optitype_hlahd.nf.test.snap index 49c1d59..3c17bea 100644 --- a/tests/optitype_hlahd.nf.test.snap +++ b/tests/optitype_hlahd.nf.test.snap @@ -38,687 +38,6 @@ "hlahd/SAMPLE_FASTQ/SAMPLE_FASTQ_final.result.txt", "hlahd/SAMPLE_FASTQ_RNA", "hlahd/SAMPLE_FASTQ_RNA/SAMPLE_FASTQ_RNA_final.result.txt", - "hlahd/hlahd", - "hlahd/hlahd/1.7.1", - "hlahd/hlahd/1.7.1/._HLA_gene.split.3.32.0.txt", - "hlahd/hlahd/1.7.1/HLA_gene.split.3.32.0.txt", - "hlahd/hlahd/1.7.1/HLA_gene.split.3.50.0.txt", - 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"hla_reference_rna.fasta.lf.drv:md5,2b70a39065cb4cebcb61c4fbe58ed80d", - "hla_reference_rna.fasta.lf.pst:md5,c4953215c2d6ca2d0778f7beac6cb112", - "hla_reference_rna.fasta.rid.concat:md5,265a1473f4582251df3a7e8cfac2c9d4", - "hla_reference_rna.fasta.rid.limits:md5,fccc5296404a012cfd5f4b99242250db", - "hla_reference_rna.fasta.sa.ind:md5,7a8a7f1ca8fbe7ee5409cf0a0337ad9c", - "hla_reference_rna.fasta.sa.len:md5,a9b77a9d99a950a3e8ac16709144c6db", - "hla_reference_rna.fasta.sa.val:md5,2aff12256a8f936264d0d843ccd2fd97", - "hla_reference_rna.fasta.txt.concat:md5,d3975911cdc2d224763528f1a08773fe", - "hla_reference_rna.fasta.txt.limits:md5,6be3fe29235eac6f36ecee28eba11697", - "hla_reference_rna.fasta.txt.size:md5,5b932358d7f42f3a5b52a4e567020d85" + "SAMPLE_FASTQ_RNA_final.result.txt:md5,15e8f8fe058169c02f4136e092981500" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-30T12:23:48.906216345" + "timestamp": "2026-02-27T11:38:08.906639716" } } \ No newline at end of file diff --git a/tests/rna.nf.test.snap b/tests/rna.nf.test.snap index 342c7cb..f4918ca 100644 --- a/tests/rna.nf.test.snap +++ b/tests/rna.nf.test.snap @@ -92,47 +92,16 @@ "optitype/SAMPLE_RNA/SAMPLE_RNA_coverage_plot.pdf", "optitype/SAMPLE_RNA/SAMPLE_RNA_result.tsv", "pipeline_info", - "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml", - "yara", - "yara/SAMPLE_RNA", - "yara/SAMPLE_RNA/SAMPLE_RNA_1.mapped.bam", - "yara/SAMPLE_RNA/SAMPLE_RNA_1.mapped.bam.bai", - "yara/SAMPLE_RNA/SAMPLE_RNA_2.mapped.bam", - "yara/SAMPLE_RNA/SAMPLE_RNA_2.mapped.bam.bai", - "yara/SAMPLE_RNA/versions.yml", - "yara/hla_reference_rna.fasta.lf.drp", - "yara/hla_reference_rna.fasta.lf.drs", - "yara/hla_reference_rna.fasta.lf.drv", - "yara/hla_reference_rna.fasta.lf.pst", - "yara/hla_reference_rna.fasta.rid.concat", - "yara/hla_reference_rna.fasta.rid.limits", - "yara/hla_reference_rna.fasta.sa.ind", - "yara/hla_reference_rna.fasta.sa.len", - "yara/hla_reference_rna.fasta.sa.val", - "yara/hla_reference_rna.fasta.txt.concat", - "yara/hla_reference_rna.fasta.txt.limits", - "yara/hla_reference_rna.fasta.txt.size" + "pipeline_info/nf_core_hlatyping_software_mqc_versions.yml" ], [ - "versions.yml:md5,3d67d5a34bf0044c6567763154ac1719", - "hla_reference_rna.fasta.lf.drp:md5,128d936b51ae31a29180daafcfcdd268", - "hla_reference_rna.fasta.lf.drs:md5,8666683506aacd900bbd5a74ac4edf68", - "hla_reference_rna.fasta.lf.drv:md5,2b70a39065cb4cebcb61c4fbe58ed80d", - "hla_reference_rna.fasta.lf.pst:md5,c4953215c2d6ca2d0778f7beac6cb112", - "hla_reference_rna.fasta.rid.concat:md5,265a1473f4582251df3a7e8cfac2c9d4", - "hla_reference_rna.fasta.rid.limits:md5,fccc5296404a012cfd5f4b99242250db", - "hla_reference_rna.fasta.sa.ind:md5,7a8a7f1ca8fbe7ee5409cf0a0337ad9c", - "hla_reference_rna.fasta.sa.len:md5,a9b77a9d99a950a3e8ac16709144c6db", - "hla_reference_rna.fasta.sa.val:md5,2aff12256a8f936264d0d843ccd2fd97", - "hla_reference_rna.fasta.txt.concat:md5,d3975911cdc2d224763528f1a08773fe", - "hla_reference_rna.fasta.txt.limits:md5,6be3fe29235eac6f36ecee28eba11697", - "hla_reference_rna.fasta.txt.size:md5,5b932358d7f42f3a5b52a4e567020d85" + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-30T13:44:47.7510918" + "timestamp": "2026-02-27T10:51:10.67594648" } } \ No newline at end of file diff --git a/workflows/hlatyping.nf b/workflows/hlatyping.nf index 97307ab..156646c 100644 --- a/workflows/hlatyping.nf +++ b/workflows/hlatyping.nf @@ -17,6 +17,7 @@ include { CHECK_PAIRED } from '../modules/local/check_paired' include { HLAHD_INSTALL } from '../modules/local/hlahd/install' include { HLAHD } from '../modules/local/hlahd/genotype' +include { HLALA_DOWNLOAD } from '../modules/local/hlala/download' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' @@ -37,6 +38,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main' include { GUNZIP } from '../modules/nf-core/gunzip/main' include { OPTITYPE } from '../modules/nf-core/optitype/main' include { SAMTOOLS_COLLATEFASTQ } from '../modules/nf-core/samtools/collatefastq/main' +include { HLALA_TYPING } from '../modules/nf-core/hlala/typing/main' include { SAMTOOLS_VIEW } from '../modules/nf-core/samtools/view/main' include { YARA_INDEX } from '../modules/nf-core/yara/index/main' include { YARA_MAPPER } from '../modules/nf-core/yara/mapper/main' @@ -71,6 +73,15 @@ workflow HLATYPING { } .set { ch_input_files } + // Create separate BAM channels for different processing paths + // One for conversion to FASTQ (OptiType/HLA-HD), one for HLA*LA (direct BAM input) + ch_input_files.bam + .multiMap { meta, files -> + for_fastq_conversion: [meta, files] + for_hlala: [meta, files] + } + .set { ch_bam_split } + // // MODULE: Concatenate FastQ files from same sample if required // @@ -79,7 +90,7 @@ workflow HLATYPING { ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) // determine BAM pairedness for fastq conversion - CHECK_PAIRED (ch_input_files.bam ) + CHECK_PAIRED (ch_bam_split.for_fastq_conversion ) CHECK_PAIRED.out.reads .map {meta, reads, single_end -> meta["single_end"] = single_end.text.toBoolean() @@ -180,14 +191,16 @@ workflow HLATYPING { ch_versions = ch_versions.mix(OPTITYPE.out.versions) } + // Parse software metadata for HLA-HD and HLA*LA + def software_meta_file = file("$projectDir/assets/software_meta.json", checkIfExists: true) + def jsonSlurper = new groovy.json.JsonSlurper() + def software_meta = jsonSlurper.parse(software_meta_file) + if ( "hlahd" in tools.tokenize(",") ) { // // MODULE: Run HLAHD typing // - // Parse HLA-HD software metadata and create installation channel - def hlahd_software_meta = file("$projectDir/assets/hlahd_software_meta.json", checkIfExists: true) - def jsonSlurper = new groovy.json.JsonSlurper() - def hlahd_meta = jsonSlurper.parse(hlahd_software_meta)['hlahd'] + def hlahd_meta = software_meta['hlahd'] def ch_hlahd_install = channel.of([ 'hlahd', hlahd_meta.version, @@ -201,6 +214,50 @@ workflow HLATYPING { ch_versions = ch_versions.mix(HLAHD.out.versions) } + if ( "hlala" in tools.tokenize(",") ) { + // + // MODULE: Run HLA*LA typing (requires BAM input) + // + // Recompress BAM to BGZF format and create index in one step + ch_bam_split.for_hlala + .map { meta, files -> [meta, files, []] } // Add empty index + .set { ch_hlala_input } + + SAMTOOLS_VIEW( + ch_hlala_input, + [[:], []], // No reference needed for BAM->BAM + [], // No qname file + 'bai' // Create BAI index + ) + ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first()) + + // Combine BAM with its index for HLA*LA + SAMTOOLS_VIEW.out.bam + .join(SAMTOOLS_VIEW.out.bai) + .set { ch_bam_with_index } + + // Graph acquisition: use pre-built directory, provided tarball, or download + def hlala_meta = software_meta['hlala'] + if (params.hlala_graph_dir) { + ch_graph_dir = channel.value(file(params.hlala_graph_dir, checkIfExists: true)) + } else { + def graph_tarball = params.hlala_graph_tarball ? + file(params.hlala_graph_tarball, checkIfExists: true) : + file('NO_FILE') + HLALA_DOWNLOAD(channel.of([hlala_meta.graph, hlala_meta.graph_url, hlala_meta.graph_md5, graph_tarball])) + ch_graph_dir = HLALA_DOWNLOAD.out.graph + ch_versions = ch_versions.mix(HLALA_DOWNLOAD.out.versions.first()) + } + + // Combine BAM+BAI with graph for HLALA_TYPING + ch_bam_with_index + .combine(ch_graph_dir) + .set { ch_hlala_typing_input } + + HLALA_TYPING(ch_hlala_typing_input) + ch_versions = ch_versions.mix(HLALA_TYPING.out.versions.first()) + } + // // Collate and save software versions //