From 7ce931f0545d7c00041ed8ae05b42c2ad3a45c28 Mon Sep 17 00:00:00 2001 From: louislenezet Date: Fri, 22 May 2026 10:14:49 +0000 Subject: [PATCH 1/3] Update to topics --- modules/nf-core/hostile/clean/main.nf | 32 +---- modules/nf-core/hostile/clean/meta.yml | 32 +++-- .../nf-core/hostile/clean/tests/main.nf.test | 19 +-- .../hostile/clean/tests/main.nf.test.snap | 131 +++++++++--------- 4 files changed, 96 insertions(+), 118 deletions(-) diff --git a/modules/nf-core/hostile/clean/main.nf b/modules/nf-core/hostile/clean/main.nf index 06c7d1c7e346..aa087d247493 100644 --- a/modules/nf-core/hostile/clean/main.nf +++ b/modules/nf-core/hostile/clean/main.nf @@ -14,7 +14,7 @@ process HOSTILE_CLEAN { output: tuple val(meta), path('*.fastq.gz'), emit: fastq tuple val(meta), path('*.json') , emit: json - path 'versions.yml' , emit: versions + tuple val("${task.process}"), val('hostile'), eval("hostile --version"), emit: versions_hostile, topic: versions when: task.ext.when == null || task.ext.when @@ -39,42 +39,16 @@ process HOSTILE_CLEAN { --reorder \\ --airplane \\ | tee > ${prefix}.json - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hostile: \$(hostile --version) - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sorted_reads = meta.single_end ? [reads].flatten() : reads.sort { read -> read.simpleName } - def reads_cmd = meta.single_end ? "--fastq1 ${sorted_reads[0]}" : "--fastq1 ${sorted_reads[0]} --fastq2 ${sorted_reads[1]}" - def fake_read2 = !meta.single_end ? "echo '' | gzip -c > ${prefix}.clean_2.fastq.gz" : "" + def fake_read2 = !meta.single_end ? "echo '' | gzip > ${prefix}.clean_2.fastq.gz" : "" """ export HOSTILE_CACHE_DIR=${reference_dir} - - echo "hostile \\ - clean \\ - ${args} \\ - --threads ${task.cpus} \\ - ${reads_cmd} \\ - --index ${reference_name} \\ - --output . \\ - --reorder \\ - --airplane \\ - | tee > ${prefix}.json" - - export HOSTILE_CACHE_DIR=${reference_dir} - echo "" | gzip -c > ${prefix}.clean_1.fastq.gz + echo "" | gzip > ${prefix}.clean_1.fastq.gz ${fake_read2} touch ${prefix}.json - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hostile: \$(hostile --version) - END_VERSIONS """ } diff --git a/modules/nf-core/hostile/clean/meta.yml b/modules/nf-core/hostile/clean/meta.yml index 121d53c81027..89220c2fcea2 100644 --- a/modules/nf-core/hostile/clean/meta.yml +++ b/modules/nf-core/hostile/clean/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "hostile_clean" description: Removes host reads from short- and long-read FASTQ sequencing files keywords: @@ -14,9 +13,9 @@ tools: documentation: "https://github.com/bede/hostile" tool_dev_url: "https://github.com/bede/hostile" doi: "10.1093/bioinformatics/btad728" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:hostile - input: - - meta: type: map @@ -41,7 +40,6 @@ input: indices AND explicitly specify `--aligner bowtie2` ontologies: - edam: "http://edamontology.org/data_1049" - output: fastq: - - meta: @@ -69,13 +67,27 @@ output: pattern: "*.json" ontologies: - edam: "http://edamontology.org/format_3464" + versions_hostile: + - - ${task.process}: + type: string + description: The name of the process + - hostile: + type: string + description: The name of the tool + - hostile --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 + - hostile: + type: string + description: The name of the tool + - hostile --version: + type: eval + description: The expression to obtain the version of the tool authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hostile/clean/tests/main.nf.test b/modules/nf-core/hostile/clean/tests/main.nf.test index 0c671d23d227..116f28f3de08 100644 --- a/modules/nf-core/hostile/clean/tests/main.nf.test +++ b/modules/nf-core/hostile/clean/tests/main.nf.test @@ -46,12 +46,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.fastq, - process.out.versions, - path(process.out.versions.get(0)).yaml, - path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')} - ).match() } + { assert path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')} }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys:["json"])).match() } ) } @@ -80,12 +76,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.fastq, - process.out.versions, - path(process.out.versions.get(0)).yaml, - path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')} - ).match() } + { assert path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')} }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys:["json"])).match() } ) } @@ -113,8 +105,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert path(process.out.versions.get(0)).yaml} + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/hostile/clean/tests/main.nf.test.snap b/modules/nf-core/hostile/clean/tests/main.nf.test.snap index 41e8ea40e29e..42d158988bcc 100644 --- a/modules/nf-core/hostile/clean/tests/main.nf.test.snap +++ b/modules/nf-core/hostile/clean/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "fastq - single-end - stub": { "content": [ { - "0": [ + "fastq": [ [ { "id": "test", @@ -11,7 +11,7 @@ "test.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "1": [ + "json": [ [ { "id": "test", @@ -20,93 +20,94 @@ "test.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ - "versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f" - ], + "versions_hostile": [ + [ + "HOSTILE_CLEAN", + "hostile", + "2.0.2" + ] + ] + } + ], + "timestamp": "2026-05-22T10:10:32.316335997", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "fastq - paired-end": { + "content": [ + { "fastq": [ [ { "id": "test", - "single_end": true + "single_end": false }, - "test.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + "test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2", + "test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7" + ] ] ], "json": [ [ { "id": "test", - "single_end": true + "single_end": false }, - "test.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.json" ] ], - "versions": [ - "versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f" - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-11T19:36:13.16472899" - }, - "fastq - paired-end": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + "versions_hostile": [ [ - "test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2", - "test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7" + "HOSTILE_CLEAN", + "hostile", + "2.0.2" ] ] - ], - [ - "versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f" - ], - { - "HOSTILE_CLEAN": { - "hostile": "2.0.2" - } - }, - true + } ], + "timestamp": "2026-05-22T10:13:45.740888243", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" - }, - "timestamp": "2025-11-09T16:15:42.374481236" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "fastq - single-end": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17" - ] - ], - [ - "versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f" - ], { - "HOSTILE_CLEAN": { - "hostile": "2.0.2" - } - }, - true + "fastq": [ + [ + { + "id": "test", + "single_end": true + }, + "test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17" + ] + ], + "json": [ + [ + { + "id": "test", + "single_end": true + }, + "test.json" + ] + ], + "versions_hostile": [ + [ + "HOSTILE_CLEAN", + "hostile", + "2.0.2" + ] + ] + } ], + "timestamp": "2026-05-22T10:13:22.374303854", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T09:45:14.395763629" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file From 77ed7a33976ac6314ee52470b669de796c79c4f9 Mon Sep 17 00:00:00 2001 From: louislenezet Date: Fri, 22 May 2026 10:46:14 +0000 Subject: [PATCH 2/3] Update to topics --- modules/nf-core/hostile/fetch/main.nf | 13 +--- modules/nf-core/hostile/fetch/meta.yml | 38 +++++++----- .../nf-core/hostile/fetch/tests/main.nf.test | 6 +- .../hostile/fetch/tests/main.nf.test.snap | 61 ++++++------------- 4 files changed, 45 insertions(+), 73 deletions(-) diff --git a/modules/nf-core/hostile/fetch/main.nf b/modules/nf-core/hostile/fetch/main.nf index 9e1df86e3832..b0aa69506b86 100644 --- a/modules/nf-core/hostile/fetch/main.nf +++ b/modules/nf-core/hostile/fetch/main.nf @@ -11,7 +11,7 @@ process HOSTILE_FETCH { output: tuple val(index_name), path('reference/'), emit: reference - path 'versions.yml', emit: versions + tuple val("${task.process}"), val('hostile'), eval("hostile --version"), emit: versions_hostile, topic: versions when: task.ext.when == null || task.ext.when @@ -27,18 +27,12 @@ process HOSTILE_FETCH { fetch \\ --name ${index_name} \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hostile: \$(hostile --version) - END_VERSIONS """ stub: """ mkdir reference/ export HOSTILE_CACHE_DIR=./reference - touch reference/human-t2t-hla.1.bt2 touch reference/human-t2t-hla.2.bt2 touch reference/human-t2t-hla.3.bt2 @@ -46,10 +40,5 @@ process HOSTILE_FETCH { touch reference/human-t2t-hla.rev.1.bt2 touch reference/human-t2t-hla.rev.2.bt2 touch reference/human-t2t-hla.mmi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hostile: \$(hostile --version) - END_VERSIONS """ } diff --git a/modules/nf-core/hostile/fetch/meta.yml b/modules/nf-core/hostile/fetch/meta.yml index bfd27f930ad2..339974db1a6d 100644 --- a/modules/nf-core/hostile/fetch/meta.yml +++ b/modules/nf-core/hostile/fetch/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "hostile_fetch" description: Downloads required reference genomes for Hostile keywords: @@ -13,14 +12,13 @@ tools: documentation: "https://github.com/bede/hostile" tool_dev_url: "https://github.com/bede/hostile" doi: "10.1093/bioinformatics/btad728" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:hostile - input: - index_name: type: string description: Name of the reference genome index to download - output: reference: - - index_name: @@ -28,20 +26,32 @@ output: description: Name of the reference genome index downloaded - reference/: type: directory - description: Directory containing required reference genome files for hostile - clean + description: Directory containing required reference genome files for + hostile clean pattern: "reference/" ontologies: - edam: "http://edamontology.org/data_1049" - + versions_hostile: + - - ${task.process}: + type: string + description: The name of the process + - hostile: + type: string + description: The name of the tool + - hostile --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 + - hostile: + type: string + description: The name of the tool + - hostile --version: + type: eval + description: The expression to obtain the version of the tool authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hostile/fetch/tests/main.nf.test b/modules/nf-core/hostile/fetch/tests/main.nf.test index bccf80491567..c2ea9118d582 100644 --- a/modules/nf-core/hostile/fetch/tests/main.nf.test +++ b/modules/nf-core/hostile/fetch/tests/main.nf.test @@ -26,8 +26,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert path(process.out.versions.get(0)).yaml} + { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -51,8 +50,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert path(process.out.versions.get(0)).yaml} + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/hostile/fetch/tests/main.nf.test.snap b/modules/nf-core/hostile/fetch/tests/main.nf.test.snap index 416b5aa71cf8..66284f07d38f 100644 --- a/modules/nf-core/hostile/fetch/tests/main.nf.test.snap +++ b/modules/nf-core/hostile/fetch/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "human-t2t-hla - bowtie2": { "content": [ { - "0": [ + "reference": [ [ "human-t2t-hla", [ @@ -15,37 +15,25 @@ ] ] ], - "1": [ - "versions.yml:md5,7a2832746463207d282bbdfb49639556" - ], - "reference": [ + "versions_hostile": [ [ - "human-t2t-hla", - [ - "human-t2t-hla.1.bt2:md5,b481b623a14908f29c5dce42077f8763", - "human-t2t-hla.2.bt2:md5,8df357276c7c3a4e768ecd70ca951b53", - "human-t2t-hla.3.bt2:md5,78289afb436f8d0a9526ecfa95e3fa24", - "human-t2t-hla.4.bt2:md5,198badf146cd0b3886b674424250d419", - "human-t2t-hla.rev.1.bt2:md5,34c65db94aba9cc49cb31e14d2698c1c", - "human-t2t-hla.rev.2.bt2:md5,53c9901609915475a2e1b009046d8371" - ] + "HOSTILE_FETCH", + "hostile", + "2.0.2" ] - ], - "versions": [ - "versions.yml:md5,7a2832746463207d282bbdfb49639556" ] } ], + "timestamp": "2026-05-22T10:17:43.280616381", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T08:37:12.533681861" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "human-t2t-hla - stub": { "content": [ { - "0": [ + "reference": [ [ "human-t2t-hla", [ @@ -59,32 +47,19 @@ ] ] ], - "1": [ - "versions.yml:md5,7a2832746463207d282bbdfb49639556" - ], - "reference": [ + "versions_hostile": [ [ - "human-t2t-hla", - [ - "human-t2t-hla.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "human-t2t-hla.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "human-t2t-hla.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "human-t2t-hla.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "human-t2t-hla.mmi:md5,d41d8cd98f00b204e9800998ecf8427e", - "human-t2t-hla.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "human-t2t-hla.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "HOSTILE_FETCH", + "hostile", + "2.0.2" ] - ], - "versions": [ - "versions.yml:md5,7a2832746463207d282bbdfb49639556" ] } ], + "timestamp": "2026-05-22T10:45:40.756531067", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T08:38:20.038803148" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file From 6ff22a7e8236538153b6c7a39cfab1f8ade306c3 Mon Sep 17 00:00:00 2001 From: louislenezet Date: Tue, 26 May 2026 14:44:29 +0000 Subject: [PATCH 3/3] Update test --- .../nf-core/fastq_fetch_clean_hostile/main.nf | 10 +- .../fastq_fetch_clean_hostile/meta.yml | 4 - .../tests/main.nf.test | 15 +- .../tests/main.nf.test.snap | 167 ++++++++++++------ 4 files changed, 115 insertions(+), 81 deletions(-) diff --git a/subworkflows/nf-core/fastq_fetch_clean_hostile/main.nf b/subworkflows/nf-core/fastq_fetch_clean_hostile/main.nf index 66d23868f81d..c071359b97da 100644 --- a/subworkflows/nf-core/fastq_fetch_clean_hostile/main.nf +++ b/subworkflows/nf-core/fastq_fetch_clean_hostile/main.nf @@ -9,7 +9,6 @@ workflow FASTQ_FETCH_CLEAN_HOSTILE { index_name // val (optional) main: - ch_versions = channel.empty() if (!index_name && !ch_reference) { error "Provide either the reference index name for HOSTILE_FETCH or an existing reference path for HOSTILE_CLEAN." @@ -22,18 +21,15 @@ workflow FASTQ_FETCH_CLEAN_HOSTILE { if (index_name) { HOSTILE_FETCH( index_name ) out_reference = HOSTILE_FETCH.out.reference - ch_versions = ch_versions.mix(HOSTILE_FETCH.out.versions.first()) } else { out_reference = ch_reference } HOSTILE_CLEAN( ch_reads, out_reference ) - ch_versions = ch_versions.mix(HOSTILE_CLEAN.out.versions.first()) emit: - reference = out_reference // channel: [ val(reference_name), path(reference_dir) ] - fastq = HOSTILE_CLEAN.out.fastq // channel: [ val(meta), [ *.fastq.gz ] ] - json = HOSTILE_CLEAN.out.json // channel: [ val(meta), [ *.json ] ] - versions = ch_versions // channel: [ versions.yml ] + reference = out_reference // channel: [ val(reference_name), path(reference_dir) ] + fastq = HOSTILE_CLEAN.out.fastq // channel: [ val(meta), [ *.fastq.gz ] ] + json = HOSTILE_CLEAN.out.json // channel: [ val(meta), [ *.json ] ] } diff --git a/subworkflows/nf-core/fastq_fetch_clean_hostile/meta.yml b/subworkflows/nf-core/fastq_fetch_clean_hostile/meta.yml index a50c52330a7e..38ae86696047 100644 --- a/subworkflows/nf-core/fastq_fetch_clean_hostile/meta.yml +++ b/subworkflows/nf-core/fastq_fetch_clean_hostile/meta.yml @@ -51,10 +51,6 @@ output: Channel containing sample metadata and Hostile cleaning log in JSON format. Structure: [ val(meta), path(*.json) ] pattern: "*.json" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" authors: - "@maia-munteanu" maintainers: diff --git a/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test b/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test index 10fc6a50a660..f00a10602295 100644 --- a/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test @@ -44,10 +44,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.fastq, - workflow.out.versions.collect{ path(it).yaml }.unique() - ).match() } + { assert snapshot(sanitizeOutput(workflow.out, unstableKeys: ["json"])).match() } ) } } @@ -72,10 +69,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.fastq, - workflow.out.versions.collect{ path(it).yaml }.unique() - ).match() } + { assert snapshot(sanitizeOutput(workflow.out, unstableKeys: ["json"])).match() } ) } } @@ -100,10 +94,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.fastq, - workflow.out.versions.collect{ path(it).yaml }.unique() - ).match() } + { assert snapshot(sanitizeOutput(workflow.out)).match() } ) } } diff --git a/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test.snap index f47173dcfada..7ff2e26b6111 100644 --- a/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test.snap @@ -1,80 +1,131 @@ { "fastq - single-end - with reference - stub": { "content": [ - [ - [ - { - "id": "test_single", - "single_end": true - }, - "test_single.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + { + "fastq": [ + [ + { + "id": "test_single", + "single_end": true + }, + "test_single.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "json": [ + [ + { + "id": "test_single", + "single_end": true + }, + "test_single.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reference": [ + [ + "genome", + [ + "genome.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] - ], - [ - { - "FASTQ_FETCH_CLEAN_HOSTILE:HOSTILE_CLEAN": { - "hostile": "2.0.2" - } - } - ] + } ], + "timestamp": "2026-05-26T14:30:20.029664659", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" - }, - "timestamp": "2025-11-10T09:37:58.736062" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "fastq - single-end - with reference": { "content": [ - [ - [ - { - "id": "test_single", - "single_end": true - }, - "test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17" + { + "fastq": [ + [ + { + "id": "test_single", + "single_end": true + }, + "test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17" + ] + ], + "json": [ + [ + { + "id": "test_single", + "single_end": true + }, + "test_single.json" + ] + ], + "reference": [ + [ + "genome", + [ + "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", + "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", + "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", + "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", + "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" + ] + ] ] - ], - [ - { - "FASTQ_FETCH_CLEAN_HOSTILE:HOSTILE_CLEAN": { - "hostile": "2.0.2" - } - } - ] + } ], + "timestamp": "2026-05-26T14:43:39.771257929", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" - }, - "timestamp": "2025-11-10T09:37:39.689986" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "fastq - paired-end - with reference": { "content": [ - [ - [ - { - "id": "test_paired", - "single_end": false - }, + { + "fastq": [ + [ + { + "id": "test_paired", + "single_end": false + }, + [ + "test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2", + "test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7" + ] + ] + ], + "json": [ + [ + { + "id": "test_paired", + "single_end": false + }, + "test_paired.json" + ] + ], + "reference": [ [ - "test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2", - "test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7" + "genome", + [ + "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", + "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", + "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", + "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", + "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" + ] ] ] - ], - [ - { - "FASTQ_FETCH_CLEAN_HOSTILE:HOSTILE_CLEAN": { - "hostile": "2.0.2" - } - } - ] + } ], + "timestamp": "2026-05-26T14:44:03.047395234", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" - }, - "timestamp": "2025-11-10T09:37:51.783759" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file