From 33c6e0cf435f9937e114c67fa4e891a39c170f66 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Sat, 7 Feb 2026 23:29:15 +0100 Subject: [PATCH 01/10] Check if output files are available before zipping them --- modules/nf-core/paraphase/main.nf | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/modules/nf-core/paraphase/main.nf b/modules/nf-core/paraphase/main.nf index 27d131214fbc..9dece58a7416 100644 --- a/modules/nf-core/paraphase/main.nf +++ b/modules/nf-core/paraphase/main.nf @@ -40,17 +40,19 @@ process PARAPHASE { $config_file \\ --out . - for vcf in ${prefix}_paraphase_vcfs/*.vcf; - do - bgzip \\ - $args2 \\ - --threads $task.cpus \\ - \$vcf; - tabix \\ - $args3 \\ - --threads $task.cpus \\ - \$vcf.gz; - done + if compgen -G "${prefix}_paraphase_vcfs/*.vcf" > /dev/null; then + for vcf in ${prefix}_paraphase_vcfs/*.vcf; + do + bgzip \\ + $args2 \\ + --threads $task.cpus \\ + \$vcf; + tabix \\ + $args3 \\ + --threads $task.cpus \\ + \$vcf.gz; + done + fi cat <<-END_VERSIONS > versions.yml "${task.process}": From 26dd4871675b9ba2ed071516f4fdfd7aa1b519f8 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Sun, 8 Feb 2026 01:04:57 +0100 Subject: [PATCH 02/10] Add test config to produce no vcf/vcf_index output --- modules/nf-core/paraphase/tests/nextflow.no_vcf.config | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 modules/nf-core/paraphase/tests/nextflow.no_vcf.config diff --git a/modules/nf-core/paraphase/tests/nextflow.no_vcf.config b/modules/nf-core/paraphase/tests/nextflow.no_vcf.config new file mode 100644 index 000000000000..c700117e8d42 --- /dev/null +++ b/modules/nf-core/paraphase/tests/nextflow.no_vcf.config @@ -0,0 +1,5 @@ +process { + withName: 'PARAPHASE' { + ext.args = '--gene RIMBP3B' + } +} From 5ac09456ba6035f45f50cb99c7276bc1ea50180d Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Sun, 8 Feb 2026 01:07:25 +0100 Subject: [PATCH 03/10] Add test to verify no vcf/vcf_index output --- modules/nf-core/paraphase/tests/main.nf.test | 37 ++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/modules/nf-core/paraphase/tests/main.nf.test b/modules/nf-core/paraphase/tests/main.nf.test index e57a0f807534..8aac3066b28c 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test +++ b/modules/nf-core/paraphase/tests/main.nf.test @@ -100,6 +100,43 @@ nextflow_process { } } + test("homo_sapiens - [ bam, bai ], no_vcf") { + + config "./nextflow.no_vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true), + ] + input[1] = TABIX_BGZIP.out.output + input[2] = [ + [ id:'test_config' ], + file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf?.isEmpty() }, + { assert process.out.vcf_index?.isEmpty() }, + { assert snapshot( + file(process.out.json.get(0).get(1)).readLines()[0..28], + process.out.bam.get(0).get(1).isEmpty(), + file(process.out.bai.get(0).get(1)).name, + process.out.versions + ).match() + } + ) + } + } + test("homo_sapiens - [ bam, bai ], config - csi_index") { config "./nextflow.csi_index.config" From 9f3bfeffb42c574c4394319e9387c8c18f976ea9 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Mon, 9 Feb 2026 19:32:28 +0100 Subject: [PATCH 04/10] Update package versions --- modules/nf-core/paraphase/environment.yml | 4 ++-- modules/nf-core/paraphase/main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/paraphase/environment.yml b/modules/nf-core/paraphase/environment.yml index f4133eecbcb5..5eb292a43706 100644 --- a/modules/nf-core/paraphase/environment.yml +++ b/modules/nf-core/paraphase/environment.yml @@ -8,6 +8,6 @@ dependencies: # renovate: datasource=conda depName=bioconda/minimap2 - bioconda::minimap2=2.30 # renovate: datasource=conda depName=bioconda/paraphase - - bioconda::paraphase=3.3.4 + - bioconda::paraphase=3.4.0 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.22.1 + - bioconda::samtools=1.23 diff --git a/modules/nf-core/paraphase/main.nf b/modules/nf-core/paraphase/main.nf index 9dece58a7416..6d72f070ad5f 100644 --- a/modules/nf-core/paraphase/main.nf +++ b/modules/nf-core/paraphase/main.nf @@ -6,7 +6,7 @@ process PARAPHASE { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/65/65e79cfe3a98637330bad85befbbb0baf72366040ce1911f60be8485eae28d55/data': - 'community.wave.seqera.io/library/minimap2_paraphase_samtools:ab39f9ad1f898e08' }" + 'community.wave.seqera.io/library/minimap2_paraphase_samtools:5cc32e174d09f608' }" input: tuple val(meta), path(bam), path(bai) From 4398b109606735d91cce83336850007d83b91e8b Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Wed, 18 Feb 2026 14:08:20 +0100 Subject: [PATCH 05/10] Update paraphase to use topic channels --- modules/nf-core/paraphase/main.nf | 4 +- modules/nf-core/paraphase/meta.yml | 75 +++++++++++++++++++++++++----- 2 files changed, 66 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/paraphase/main.nf b/modules/nf-core/paraphase/main.nf index 6d72f070ad5f..58c98c5773ac 100644 --- a/modules/nf-core/paraphase/main.nf +++ b/modules/nf-core/paraphase/main.nf @@ -19,7 +19,9 @@ process PARAPHASE { tuple val(meta), path("*.paraphase.bam.bai") , emit: bai tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz") , emit: vcf , optional: true tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}"), emit: vcf_index, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('minimap2'), eval('minimap2 --version') , emit: versions_minimap2 , topic: versions + tuple val("${task.process}"), val('paraphase'), eval('paraphase --version') , emit: versions_paraphase , topic: versions + tuple val("${task.process}"), val('samtools'), eval('samtools --version') , emit: versions_samtools , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/paraphase/meta.yml b/modules/nf-core/paraphase/meta.yml index 424293dec13e..924f3b41ada0 100644 --- a/modules/nf-core/paraphase/meta.yml +++ b/modules/nf-core/paraphase/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "paraphase" description: "HiFi-based caller for highly homologous genes" keywords: @@ -12,9 +11,9 @@ tools: documentation: "https://github.com/PacificBiosciences/paraphase" tool_dev_url: "https://github.com/PacificBiosciences/paraphase" doi: "10.1016/j.ajhg.2023.01.001" - licence: ["BSD-3-clause-Clear"] + licence: + - "BSD-3-clause-Clear" identifier: "" - input: - - meta: type: map @@ -51,7 +50,7 @@ input: description: Config file pattern: "*.yaml" ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - edam: http://edamontology.org/format_3750 output: json: - - meta: @@ -64,7 +63,7 @@ output: description: Summary of haplotype and variant calls pattern: "*.paraphase.json" ontologies: - - edam: http://edamontology.org/format_3464 # JSON + - edam: http://edamontology.org/format_3464 bam: - - meta: type: map @@ -98,7 +97,7 @@ output: description: compressed VCF file(s) per gene pattern: "*.vcf.gz" ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 vcf_index: - - meta: type: map @@ -110,13 +109,65 @@ output: description: compressed VCF file index pattern: "*.vcf.gz.{tbi,csi}" ontologies: [] + versions_minimap2: + - - ${task.process}: + type: string + description: The name of the process + - minimap2: + type: string + description: The name of the tool + - minimap2 --version: + type: eval + description: The expression to obtain the version of the tool + versions_paraphase: + - - ${task.process}: + type: string + description: The name of the process + - paraphase: + type: string + description: The name of the tool + - paraphase --version: + type: eval + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version: + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - minimap2: + type: string + description: The name of the tool + - minimap2 --version: + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - paraphase: + type: string + description: The name of the tool + - paraphase --version: + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version: + type: eval + description: The expression to obtain the version of the tool authors: - "@fellen31" maintainers: From b0e95dba65a31b4a1e1eb8bc94f38667dccd5187 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Wed, 18 Feb 2026 21:32:26 +0100 Subject: [PATCH 06/10] Remove process.out.versions after move to topic channels --- modules/nf-core/paraphase/tests/main.nf.test | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/paraphase/tests/main.nf.test b/modules/nf-core/paraphase/tests/main.nf.test index 8aac3066b28c..5729420ac6e2 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test +++ b/modules/nf-core/paraphase/tests/main.nf.test @@ -53,8 +53,7 @@ nextflow_process { path(process.out.vcf.get(0).get(1)).vcf.summary, bam(process.out.bam.get(0).get(1)).getReadsMD5(), file(process.out.bai.get(0).get(1)).name, - file(process.out.vcf_index.get(0).get(1)).name, - process.out.versions + file(process.out.vcf_index.get(0).get(1)).name ).match() } ) @@ -92,8 +91,7 @@ nextflow_process { path(process.out.vcf.get(0).get(1)).vcf.summary, bam(process.out.bam.get(0).get(1)).getReadsMD5(), file(process.out.bai.get(0).get(1)).name, - file(process.out.vcf_index.get(0).get(1)).name, - process.out.versions + file(process.out.vcf_index.get(0).get(1)).name ).match() } ) @@ -129,8 +127,7 @@ nextflow_process { { assert snapshot( file(process.out.json.get(0).get(1)).readLines()[0..28], process.out.bam.get(0).get(1).isEmpty(), - file(process.out.bai.get(0).get(1)).name, - process.out.versions + file(process.out.bai.get(0).get(1)).name ).match() } ) @@ -167,8 +164,7 @@ nextflow_process { path(process.out.vcf.get(0).get(1)).vcf.summary, bam(process.out.bam.get(0).get(1)).getReadsMD5(), file(process.out.bai.get(0).get(1)).name, - file(process.out.vcf_index.get(0).get(1)).name, - process.out.versions + file(process.out.vcf_index.get(0).get(1)).name ).match() } ) From 54c6bc58f64bdaf29b2618052fc9655bfb22dd6a Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Wed, 18 Feb 2026 21:57:32 +0100 Subject: [PATCH 07/10] Update test snapshot --- .../nf-core/paraphase/tests/main.nf.test.snap | 211 +++++++++++++++--- 1 file changed, 176 insertions(+), 35 deletions(-) diff --git a/modules/nf-core/paraphase/tests/main.nf.test.snap b/modules/nf-core/paraphase/tests/main.nf.test.snap index bd34528e1658..4e7080c97e27 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test.snap +++ b/modules/nf-core/paraphase/tests/main.nf.test.snap @@ -46,16 +46,55 @@ "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=75, phased=true, phasedAutodetect=true]", "fcfb9a8752fedb1f49996c4fb03c7a9b", "test.paraphase.bam.bai", - "test_PRODH.vcf.gz.tbi", + "test_PRODH.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-02-18T21:54:35.607780628" + }, + "homo_sapiens - [ bam, bai ], no_vcf": { + "content": [ [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" - ] + "{", + " \"RIMBP3B\": {", + " \"total_cn\": null,", + " \"gene_cn\": null,", + " \"final_haplotypes\": null,", + " \"two_copy_haplotypes\": null,", + " \"alleles_final\": null,", + " \"haplotype_links\": null,", + " \"highest_total_cn\": null,", + " \"assembled_haplotypes\": null,", + " \"sites_for_phasing\": null,", + " \"unique_supporting_reads\": null,", + " \"het_sites_not_used_in_phasing\": null,", + " \"homozygous_sites\": null,", + " \"haplotype_details\": null,", + " \"nonunique_supporting_reads\": null,", + " \"read_details\": null,", + " \"genome_depth\": null,", + " \"region_depth\": {", + " \"median\": 0.0,", + " \"percentile80\": 0.0", + " },", + " \"sample_sex\": null,", + " \"heterozygous_sites\": null,", + " \"phase_region\": \"38:chr22:21380000-21390000\",", + " \"raw_alleles\": null,", + " \"fusions_called\": null", + " }", + "}" + ], + false, + "test.paraphase.bam.bai" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.4" }, - "timestamp": "2025-09-11T09:32:40.516830171" + "timestamp": "2026-02-18T21:55:00.725248215" }, "homo_sapiens - [ bam, bai ], config - stub": { "content": [ @@ -106,7 +145,25 @@ ] ], "5": [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" + [ + "PARAPHASE", + "minimap2", + "2.30-r1287" + ] + ], + "6": [ + [ + "PARAPHASE", + "paraphase", + "3.3.4" + ] + ], + "7": [ + [ + "PARAPHASE", + "samtools", + "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + ] ], "bai": [ [ @@ -153,16 +210,34 @@ "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" + "versions_minimap2": [ + [ + "PARAPHASE", + "minimap2", + "2.30-r1287" + ] + ], + "versions_paraphase": [ + [ + "PARAPHASE", + "paraphase", + "3.3.4" + ] + ], + "versions_samtools": [ + [ + "PARAPHASE", + "samtools", + "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-01-27T15:17:09.630618" + "timestamp": "2026-02-19T09:46:09.880880553" }, "homo_sapiens - [ bam, bai ], config - csi_index": { "content": [ @@ -211,16 +286,13 @@ "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=75, phased=true, phasedAutodetect=true]", "fcfb9a8752fedb1f49996c4fb03c7a9b", "test.paraphase.bam.bai", - "test_PRODH.vcf.gz.csi", - [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" - ] + "test_PRODH.vcf.gz.csi" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.4" }, - "timestamp": "2025-09-11T09:32:57.070356861" + "timestamp": "2026-02-18T21:55:14.674664598" }, "homo_sapiens - [ bam, bai ], [] - stub": { "content": [ @@ -271,7 +343,25 @@ ] ], "5": [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" + [ + "PARAPHASE", + "minimap2", + "2.30-r1287" + ] + ], + "6": [ + [ + "PARAPHASE", + "paraphase", + "3.3.4" + ] + ], + "7": [ + [ + "PARAPHASE", + "samtools", + "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + ] ], "bai": [ [ @@ -318,16 +408,34 @@ "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" + "versions_minimap2": [ + [ + "PARAPHASE", + "minimap2", + "2.30-r1287" + ] + ], + "versions_paraphase": [ + [ + "PARAPHASE", + "paraphase", + "3.3.4" + ] + ], + "versions_samtools": [ + [ + "PARAPHASE", + "samtools", + "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-01-27T15:17:01.824986" + "timestamp": "2026-02-19T09:45:48.96229081" }, "homo_sapiens - [ bam, bai ], config": { "content": [ @@ -376,16 +484,13 @@ "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=75, phased=true, phasedAutodetect=true]", "fcfb9a8752fedb1f49996c4fb03c7a9b", "test.paraphase.bam.bai", - "test_PRODH.vcf.gz.tbi", - [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" - ] + "test_PRODH.vcf.gz.tbi" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.4" }, - "timestamp": "2025-09-11T09:32:49.001155194" + "timestamp": "2026-02-18T21:54:49.916379631" }, "homo_sapiens - [ bam, bai ], config - stub - csi_index": { "content": [ @@ -436,7 +541,25 @@ ] ], "5": [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" + [ + "PARAPHASE", + "minimap2", + "2.30-r1287" + ] + ], + "6": [ + [ + "PARAPHASE", + "paraphase", + "3.3.4" + ] + ], + "7": [ + [ + "PARAPHASE", + "samtools", + "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + ] ], "bai": [ [ @@ -483,15 +606,33 @@ "test_stub.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,a9cce922e599432f5029bf5fb7039921" + "versions_minimap2": [ + [ + "PARAPHASE", + "minimap2", + "2.30-r1287" + ] + ], + "versions_paraphase": [ + [ + "PARAPHASE", + "paraphase", + "3.3.4" + ] + ], + "versions_samtools": [ + [ + "PARAPHASE", + "samtools", + "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-01-27T15:17:17.467148" + "timestamp": "2026-02-19T09:46:33.505093462" } } \ No newline at end of file From 03193366e3e2c1e532a90ee0498d0d3d8c48fdd8 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Thu, 19 Feb 2026 12:03:53 +0100 Subject: [PATCH 08/10] Capture only samtools' version --- modules/nf-core/paraphase/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/paraphase/main.nf b/modules/nf-core/paraphase/main.nf index 58c98c5773ac..41e2519881eb 100644 --- a/modules/nf-core/paraphase/main.nf +++ b/modules/nf-core/paraphase/main.nf @@ -21,7 +21,7 @@ process PARAPHASE { tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}"), emit: vcf_index, optional: true tuple val("${task.process}"), val('minimap2'), eval('minimap2 --version') , emit: versions_minimap2 , topic: versions tuple val("${task.process}"), val('paraphase'), eval('paraphase --version') , emit: versions_paraphase , topic: versions - tuple val("${task.process}"), val('samtools'), eval('samtools --version') , emit: versions_samtools , topic: versions + tuple val("${task.process}"), val('samtools'), eval('samtools --version | sed \'1!d;s/.* //\'') , emit: versions_samtools , topic: versions when: task.ext.when == null || task.ext.when From dbcc1c73bf7dd5de354231579e2b61ed61fda652 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Thu, 19 Feb 2026 13:07:08 +0100 Subject: [PATCH 09/10] Use sha to check json file's consistency --- modules/nf-core/paraphase/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/paraphase/tests/main.nf.test b/modules/nf-core/paraphase/tests/main.nf.test index 5729420ac6e2..6796c93ffbcb 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test +++ b/modules/nf-core/paraphase/tests/main.nf.test @@ -125,7 +125,7 @@ nextflow_process { { assert process.out.vcf?.isEmpty() }, { assert process.out.vcf_index?.isEmpty() }, { assert snapshot( - file(process.out.json.get(0).get(1)).readLines()[0..28], + file(process.out.json.get(0).get(1)), process.out.bam.get(0).get(1).isEmpty(), file(process.out.bai.get(0).get(1)).name ).match() From a0c80bf364db77068d300eb9026e41295153898a Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Thu, 19 Feb 2026 14:00:06 +0100 Subject: [PATCH 10/10] Update test snapshot --- .../nf-core/paraphase/tests/main.nf.test.snap | 52 ++++--------------- 1 file changed, 11 insertions(+), 41 deletions(-) diff --git a/modules/nf-core/paraphase/tests/main.nf.test.snap b/modules/nf-core/paraphase/tests/main.nf.test.snap index 4e7080c97e27..e0fe3ac135b9 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test.snap +++ b/modules/nf-core/paraphase/tests/main.nf.test.snap @@ -56,37 +56,7 @@ }, "homo_sapiens - [ bam, bai ], no_vcf": { "content": [ - [ - "{", - " \"RIMBP3B\": {", - " \"total_cn\": null,", - " \"gene_cn\": null,", - " \"final_haplotypes\": null,", - " \"two_copy_haplotypes\": null,", - " \"alleles_final\": null,", - " \"haplotype_links\": null,", - " \"highest_total_cn\": null,", - " \"assembled_haplotypes\": null,", - " \"sites_for_phasing\": null,", - " \"unique_supporting_reads\": null,", - " \"het_sites_not_used_in_phasing\": null,", - " \"homozygous_sites\": null,", - " \"haplotype_details\": null,", - " \"nonunique_supporting_reads\": null,", - " \"read_details\": null,", - " \"genome_depth\": null,", - " \"region_depth\": {", - " \"median\": 0.0,", - " \"percentile80\": 0.0", - " },", - " \"sample_sex\": null,", - " \"heterozygous_sites\": null,", - " \"phase_region\": \"38:chr22:21380000-21390000\",", - " \"raw_alleles\": null,", - " \"fusions_called\": null", - " }", - "}" - ], + "test.paraphase.json:md5,a6126dc93d832121a54532cfc3675027", false, "test.paraphase.bam.bai" ], @@ -94,7 +64,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-02-18T21:55:00.725248215" + "timestamp": "2026-02-19T13:48:14.010321602" }, "homo_sapiens - [ bam, bai ], config - stub": { "content": [ @@ -162,7 +132,7 @@ [ "PARAPHASE", "samtools", - "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + "1.22.1" ] ], "bai": [ @@ -228,7 +198,7 @@ [ "PARAPHASE", "samtools", - "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + "1.22.1" ] ] } @@ -237,7 +207,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-02-19T09:46:09.880880553" + "timestamp": "2026-02-19T13:59:46.344105904" }, "homo_sapiens - [ bam, bai ], config - csi_index": { "content": [ @@ -360,7 +330,7 @@ [ "PARAPHASE", "samtools", - "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + "1.22.1" ] ], "bai": [ @@ -426,7 +396,7 @@ [ "PARAPHASE", "samtools", - "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + "1.22.1" ] ] } @@ -435,7 +405,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-02-19T09:45:48.96229081" + "timestamp": "2026-02-19T13:59:33.864338702" }, "homo_sapiens - [ bam, bai ], config": { "content": [ @@ -558,7 +528,7 @@ [ "PARAPHASE", "samtools", - "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + "1.22.1" ] ], "bai": [ @@ -624,7 +594,7 @@ [ "PARAPHASE", "samtools", - "samtools 1.22.1\nUsing htslib 1.22.1\nCopyright (C) 2025 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1752528053426/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1752528053426/work=/usr/local/src/conda/samtools-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/opt/conda/libexec/htslib htscodecs=1.6.4\n CC: /opt/conda/conda-bld/htslib_1752522550715/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1752522550715/work=/usr/local/src/conda/htslib-1.22.1 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t file, preload, data\n S3 Multipart Upload:\t s3w+https, s3w+http, s3w\n Amazon S3:\t s3+https, s3, s3+http\n libcurl:\t gophers, smtp, wss, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ws, ftps, https, ftp, gopher, sftp, imap, http, smtps, scp, dict, mqtt, telnet\n Google Cloud Storage:\t gs+http, gs+https, gs\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" + "1.22.1" ] ] } @@ -633,6 +603,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-02-19T09:46:33.505093462" + "timestamp": "2026-02-19T13:59:58.984802834" } } \ No newline at end of file