From 6eff885a08a3390384cef7bfb9940bccab2e9a3a Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Thu, 18 Jun 2026 02:38:18 +0000 Subject: [PATCH 01/32] create and apply test dataset --- assets/samplesheet.csv | 5 ++--- workflows/datasync.nf | 13 +++++++++++-- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 55cd8f9..9ed843e 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,2 @@ -sample,input -human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/ -test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz +sample,input,checksum_md5,checksum_sha +demultiplex,s3://nf-core-awsmegatests/demultiplex/results-fbec8e442f0599f8b74876e62263af05b9a41d33/,checksum_md5.tsv,checksum_sha.tsv diff --git a/workflows/datasync.nf b/workflows/datasync.nf index 6e6c910..663fcc0 100644 --- a/workflows/datasync.nf +++ b/workflows/datasync.nf @@ -31,11 +31,20 @@ workflow DATASYNC { ch_versions = channel.empty() ch_multiqc_files = channel.empty() + ch_samplesheet_without_md5 = ch_samplesheet.map { meta, files -> + def filtered_files = files.findAll { file -> + !file.name.endsWith('.md5') + } + + tuple(meta, filtered_files) + } MD5SUM( - ch_samplesheet, - false + ch_samplesheet_without_md5.transpose(), + true ) + MD5SUM.output.checksum.view() + SHASUM( ch_samplesheet.transpose() ) From 7ebf53e998a2ae8174521e47853b8d7644938a50 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Thu, 18 Jun 2026 02:48:40 +0000 Subject: [PATCH 02/32] separate minimal test profile and full test profile --- assets/samplesheet.csv | 5 +++-- assets/samplesheet_full.csv | 2 ++ conf/test_full.config | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) create mode 100644 assets/samplesheet_full.csv diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 9ed843e..82e35fd 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,2 +1,3 @@ -sample,input,checksum_md5,checksum_sha -demultiplex,s3://nf-core-awsmegatests/demultiplex/results-fbec8e442f0599f8b74876e62263af05b9a41d33/,checksum_md5.tsv,checksum_sha.tsv +sample,input +human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/ +test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz \ No newline at end of file diff --git a/assets/samplesheet_full.csv b/assets/samplesheet_full.csv new file mode 100644 index 0000000..9ed843e --- /dev/null +++ b/assets/samplesheet_full.csv @@ -0,0 +1,2 @@ +sample,input,checksum_md5,checksum_sha +demultiplex,s3://nf-core-awsmegatests/demultiplex/results-fbec8e442f0599f8b74876e62263af05b9a41d33/,checksum_md5.tsv,checksum_sha.tsv diff --git a/conf/test_full.config b/conf/test_full.config index f11bc7e..b75f98c 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data for full size test // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + input = "${projectDir}/assets/samplesheet_full.csv" // Genome references genome = 'R64-1-1' From ebf569de75bd48e29411a127e58b0e8ff6edaa1b Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Thu, 18 Jun 2026 03:06:02 +0000 Subject: [PATCH 03/32] update snapshot --- tests/default.nf.test.snap | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f48ad94..a20e40d 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -14,8 +14,13 @@ }, [ "md5sum", - "md5sum/human_grch38_sequence.md5", - "md5sum/test_fastq.md5", + "md5sum/GenomeSize.xml.md5", + "md5sum/GenomeSize.xml.old.md5", + "md5sum/genome.dict.md5", + "md5sum/genome.dict.old.md5", + "md5sum/genome.fa.fai.md5", + "md5sum/genome.fa.md5", + "md5sum/test2_1.fastq.gz.md5", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -38,8 +43,13 @@ "shasum/test2_1.fastq.gz.sha256" ], [ - "human_grch38_sequence.md5:md5,0547c2f89caeb0e8e7d67da583e09d90", - "test_fastq.md5:md5,145df327e566f16b545fbca236f9bb62", + "GenomeSize.xml.md5:md5,0c1c07f13ddcd6f479f8312b0c7d9843", + "GenomeSize.xml.old.md5:md5,8273ac6aa130edf9e628cf0cf2566855", + "genome.dict.md5:md5,cf34a65ce7a3e827c66eadb2d5522551", + "genome.dict.old.md5:md5,4dfbb85cd00197e03f43f999b39addab", + "genome.fa.fai.md5:md5,8fc26b8f3ce6b83f9860ae9a2347d046", + "genome.fa.md5:md5,cca9026fcc32a789c00d9070edac5809", + "test2_1.fastq.gz.md5:md5,145df327e566f16b545fbca236f9bb62", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "GenomeSize.xml.old.sha256:md5,068e91cdcc084710caf61a0859ac2be9", "GenomeSize.xml.sha256:md5,e7a175f04cab11ce0a245133d70de9fb", @@ -50,10 +60,10 @@ "test2_1.fastq.gz.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" ] ], - "timestamp": "2026-06-16T18:04:56.374326627", + "timestamp": "2026-06-18T03:05:43.540206333", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.4" } } } \ No newline at end of file From 4d7e3c8799db643e31d22abbd8370f2eedfdbb0f Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Thu, 18 Jun 2026 03:07:50 +0000 Subject: [PATCH 04/32] fix: run prettier --- assets/samplesheet.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 82e35fd..55cd8f9 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,3 @@ sample,input human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/ -test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz \ No newline at end of file +test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz From f9abbf75ef99e0a4f43e6a89da4159f1b5f3240b Mon Sep 17 00:00:00 2001 From: delfiterradas Date: Thu, 18 Jun 2026 20:54:20 +0200 Subject: [PATCH 05/32] Remove fastqc --- conf/modules.config | 4 - modules.json | 5 - .../linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt | 822 ------------------ .../linux_arm64-bd-e455e32f745abe68_1.txt | 769 ---------------- modules/nf-core/fastqc/environment.yml | 7 - modules/nf-core/fastqc/main.nf | 57 -- modules/nf-core/fastqc/meta.yml | 111 --- modules/nf-core/fastqc/tests/main.nf.test | 309 ------- .../nf-core/fastqc/tests/main.nf.test.snap | 476 ---------- 9 files changed, 2560 deletions(-) delete mode 100644 modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt delete mode 100644 modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt delete mode 100644 modules/nf-core/fastqc/environment.yml delete mode 100644 modules/nf-core/fastqc/main.nf delete mode 100644 modules/nf-core/fastqc/meta.yml delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap diff --git a/conf/modules.config b/conf/modules.config index d203d2b..f0b0d55 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,10 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: FASTQC { - ext.args = '--quiet' - } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/modules.json b/modules.json index 13a67eb..a6c41ad 100644 --- a/modules.json +++ b/modules.json @@ -5,11 +5,6 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "fastqc": { - "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["modules"] - }, "md5sum": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", diff --git a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt deleted file mode 100644 index 7770ccd..0000000 --- a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt +++ /dev/null @@ -1,822 +0,0 @@ - -version: 6 -environments: -default: -channels: -- url: https://conda.anaconda.org/conda-forge/ -- url: https://conda.anaconda.org/bioconda/ -- url: https://conda.anaconda.org/bioconda/ -options: 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$schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index 1085126..0000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,57 +0,0 @@ -process FASTQC { - tag "${meta.id}" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' - : 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'}" - - input: - tuple val(meta), path(reads, stageAs: '?/*') - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip"), emit: zip - tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[reads, "${prefix}.${reads.extension}"]] : reads.withIndex().collect { entry, index -> [entry, "${prefix}_${index + 1}.${entry.extension}"] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect { _old_name, new_name -> new_name }.join(' ') - - // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) - // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 - // Dividing the task.memory by task.cpus allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory - ? (task.memory.toUnit('MB') / task.cpus).intValue() - : null - // FastQC memory value allowed range (100 - 10000) - def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) - def fastqc_memory_arg = fastqc_memory ? "--memory ${fastqc_memory}" : '' - - """ - printf "%s %s\\n" ${rename_to} | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - ${args} \\ - --threads ${task.cpus} \\ - ${fastqc_memory_arg} \\ - ${renamed_files} - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index 2f6cfef..0000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,111 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] - identifier: biotools:fastqc -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - ontologies: [] -output: - html: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - ontologies: [] - zip: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.zip": - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - ontologies: [] - versions_fastqc: - - - ${task.process}: - type: string - description: The process the versions were collected from - - fastqc: - type: string - description: The tool name - - fastqc --version | sed "/FastQC v/!d; s/.*v//": - type: eval - description: The expression to obtain the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - fastqc: - type: string - description: The tool name - - fastqc --version | sed "/FastQC v/!d; s/.*v//": - type: eval - description: The expression to obtain the version of the tool -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -containers: - docker: - linux/arm64: - name: community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68 - build_id: bd-e455e32f745abe68_1 - scan_id: sc-f102f736465af88c_1 - linux/amd64: - name: community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2 - build_id: bd-5cb1a2fa2f18c7c2_1 - scan_id: sc-0c0466326b6b77d2_1 - singularity: - linux/amd64: - name: oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd - build_id: bd-5c4bd442468d75dd_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data - linux/arm64: - name: oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035 - build_id: bd-127a87fc06499035_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data - conda: - linux/amd64: - lock_file: modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt - linux/arm64: - lock_file: modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 66c44da..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,309 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 paired-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 interleaved [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 paired-end [bam]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 multiple [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 custom_prefix") { - - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 single-end [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 interleaved [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [bam] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 multiple [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 custom_prefix - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index c8ee120..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,476 +0,0 @@ -{ - "sarscov2 custom_prefix": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:14.518503" - }, - "sarscov2 single-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:19.309008" - }, - "sarscov2 custom_prefix - stub": { - "content": [ - { - "0": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:44.94888" - }, - "sarscov2 interleaved [fastq]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:38:45.168496" - }, - "sarscov2 paired-end [bam]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:38:53.268919" - }, - "sarscov2 multiple [fastq]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:05.050305" - }, - "sarscov2 paired-end [fastq]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:38:37.2373" - }, - "sarscov2 paired-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:24.450398" - }, - "sarscov2 multiple [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:39.758762" - }, - "sarscov2 single-end [fastq]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:38:29.555068" - }, - "sarscov2 interleaved [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:29.193136" - }, - "sarscov2 paired-end [bam] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:34.144919" - } -} \ No newline at end of file From a4651fe348767e969d8d294e7dc35374115d1d46 Mon Sep 17 00:00:00 2001 From: delfiterradas Date: Thu, 18 Jun 2026 23:11:53 +0200 Subject: [PATCH 06/32] Stage whole directory instead of individual files to keep path structures --- .../local/utils_nfcore_datasync_pipeline/main.nf | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf index db1f6d4..b3ce127 100644 --- a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf @@ -109,16 +109,6 @@ workflow PIPELINE_INITIALISATION { channel .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) - .map { - meta, input_path -> - def target = file(input_path) - if (target.isDirectory()) { - def all_files = files("${input_path}/**", type: 'file') - [meta, all_files] - } else { - [meta, [target]] - } - } .set { ch_samplesheet } emit: From 7ea385303402d0ec4c4ca7e3c620d7c6fcb813b3 Mon Sep 17 00:00:00 2001 From: delfiterradas Date: Thu, 18 Jun 2026 23:13:32 +0200 Subject: [PATCH 07/32] Add checksum column and adapt samplesheet channel --- assets/checksum.md5 | 21 +++++++++++++++++++++ assets/samplesheet.csv | 6 +++--- assets/schema_input.json | 19 ++++++++++++++++++- workflows/datasync.nf | 18 ++++++++++++++++-- 4 files changed, 58 insertions(+), 6 deletions(-) create mode 100644 assets/checksum.md5 diff --git a/assets/checksum.md5 b/assets/checksum.md5 new file mode 100644 index 0000000..b851672 --- /dev/null +++ b/assets/checksum.md5 @@ -0,0 +1,21 @@ +6cae999421b3107d31aaee312a67b2b4 BWAIndex/genome.fa.pac +dee21a414c8c9435c516ce51453eac69 BWAIndex/genome.fa.ann +a6da8681616c05eb542f1d91606a7b2f BWAIndex/genome.fa +6cae999421b3107d31aaee312a67b2b4 BWAIndex/version0.6.0/genome.fa.pac +dee21a414c8c9435c516ce51453eac69 BWAIndex/version0.6.0/genome.fa.ann +a6da8681616c05eb542f1d91606a7b2f BWAIndex/version0.6.0/genome.fa +b5666883af79e600563852fbd6db60ff BWAIndex/version0.6.0/genome.fa.sa +54d052dc82eee7a34465b8e8a8989631 BWAIndex/version0.6.0/genome.fa.amb +88712af9626d5cbba82007cf8e3f90b2 BWAIndex/version0.6.0/genome.fa.bwt +6cae999421b3107d31aaee312a67b2b4 BWAIndex/version0.5.x/genome.fa.pac +dee21a414c8c9435c516ce51453eac69 BWAIndex/version0.5.x/genome.fa.ann +a6da8681616c05eb542f1d91606a7b2f BWAIndex/version0.5.x/genome.fa +826ca9f3dd61da0e50e869ead26edd99 BWAIndex/version0.5.x/genome.fa.rpac +08b6a8da1dae3f4d22e2e78887ddc9e4 BWAIndex/version0.5.x/genome.fa.rsa +456ac470698ac3ce1bb56110f00ac732 BWAIndex/version0.5.x/genome.fa.sa +54d052dc82eee7a34465b8e8a8989631 BWAIndex/version0.5.x/genome.fa.amb +d48c35964b0817176190aab0c8270e5d BWAIndex/version0.5.x/genome.fa.rbwt +9177d5f8c71ec47f65ccf0ab189ab408 BWAIndex/version0.5.x/genome.fa.bwt +b5666883af79e600563852fbd6db60ff BWAIndex/genome.fa.sa +54d052dc82eee7a34465b8e8a8989631 BWAIndex/genome.fa.amb +88712af9626d5cbba82007cf8e3f90b2 BWAIndex/genome.fa.bwt diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 55cd8f9..e4ef522 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,3 @@ -sample,input -human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/ -test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz +sample,input,checksum_md5 +human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/,assets/checksum.md5 +test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz,f06e81ce1eb2d5424f88ca7f345ec0d1 diff --git a/assets/schema_input.json b/assets/schema_input.json index 4afb584..e26e491 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -17,8 +17,25 @@ "type": "string", "pattern": "^\\S+$", "errorMessage": "Input path must be provided and cannot contain spaces" + }, + "checksum_md5": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Checksum_md5 cannot contain spaces" + }, + "checksum_sha": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Checksum_sha cannot contain spaces" } }, - "required": ["sample", "input"] + "required": [ + "sample", + "input" + ], + "oneOf": [ + { "required" : ["checksum_md5"] }, + { "required" : ["checksum_sha"] } + ] } } diff --git a/workflows/datasync.nf b/workflows/datasync.nf index 6e6c910..afa1194 100644 --- a/workflows/datasync.nf +++ b/workflows/datasync.nf @@ -31,13 +31,27 @@ workflow DATASYNC { ch_versions = channel.empty() ch_multiqc_files = channel.empty() + ch_samplesheet = ch_samplesheet.multiMap { + meta, input_path, md5, sha -> + input: [ meta, input_path ] + checksum: [ meta, md5, sha ] + } + + ch_checksum = ch_samplesheet.checksum.branch { + meta, md5, sha -> + md5: !md5.isEmpty() + return [ meta, md5 ] + sha: !sha.isEmpty() + return [ meta, sha ] + } + MD5SUM( - ch_samplesheet, + ch_samplesheet.input, false ) SHASUM( - ch_samplesheet.transpose() + ch_samplesheet.input ) // From 47f68bd1095d4fc2996f4924657f6bc60ea66de7 Mon Sep 17 00:00:00 2001 From: delfiterradas Date: Thu, 18 Jun 2026 23:14:07 +0200 Subject: [PATCH 08/32] Modify shasum to work with multiple files --- modules/nf-core/shasum/main.nf | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index 2fa689d..b79d387 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -8,7 +8,7 @@ process SHASUM { : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" input: - tuple val(meta), path(file) + tuple val(meta), path(files) output: tuple val(meta), path("*.sha256"), emit: checksum @@ -19,15 +19,17 @@ process SHASUM { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" """ - sha256sum \\ - ${args} \\ - ${file} \\ - > ${file}.sha256 + find -L * -type f \\ + ! -name '*.sha256' \\ + -exec sha256sum ${args} "{}" + \\ + > ${prefix}.sha256 """ stub: + def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${file}.sha256 + touch ${prefix}.sha256 """ } From 4976eb9776252d31076e00f137ff3c1d4b99ad16 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Fri, 19 Jun 2026 18:45:50 +0000 Subject: [PATCH 09/32] include test full --- conf/test_full.config | 2 +- tests/main_full.nf.test | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 tests/main_full.nf.test diff --git a/conf/test_full.config b/conf/test_full.config index b75f98c..af7be2f 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data for full size test // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = "${projectDir}/assets/samplesheet_full.csv" + input = "https://raw.githubusercontent.com/nf-core/test-datasets/datasync/test-data/samplesheet.csv" // Genome references genome = 'R64-1-1' diff --git a/tests/main_full.nf.test b/tests/main_full.nf.test new file mode 100644 index 0000000..47558e6 --- /dev/null +++ b/tests/main_full.nf.test @@ -0,0 +1,33 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + + test("-profile test_full") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assert workflow.success + assertAll( + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_datasync_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content + ).match() } + ) + } + } +} From a0543f16d66cd1ff91f3af3c1d9e90e3ea90942b Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Fri, 19 Jun 2026 18:46:10 +0000 Subject: [PATCH 10/32] remove debug print --- workflows/datasync.nf | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/workflows/datasync.nf b/workflows/datasync.nf index c9370be..a184b77 100644 --- a/workflows/datasync.nf +++ b/workflows/datasync.nf @@ -44,14 +44,12 @@ workflow DATASYNC { sha: !sha.isEmpty() return [ meta, sha ] } - + MD5SUM( ch_samplesheet.input, false ) - MD5SUM.output.checksum.view() - SHASUM( ch_samplesheet.input ) From a26b66b492d9273cc7f24149615c8efe41cd6854 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Fri, 19 Jun 2026 18:46:21 +0000 Subject: [PATCH 11/32] fix schema --- assets/schema_input.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index e26e491..7dfd8d2 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -33,7 +33,7 @@ "sample", "input" ], - "oneOf": [ + "anyOf": [ { "required" : ["checksum_md5"] }, { "required" : ["checksum_sha"] } ] From b14919e43d3a27b092f6f39aa30d0a498d873f9b Mon Sep 17 00:00:00 2001 From: zxBIB Date: Fri, 19 Jun 2026 20:57:35 +0200 Subject: [PATCH 12/32] create main_full snapshot --- tests/main_full.nf.test.snap | 49 ++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 tests/main_full.nf.test.snap diff --git a/tests/main_full.nf.test.snap b/tests/main_full.nf.test.snap new file mode 100644 index 0000000..5a799b3 --- /dev/null +++ b/tests/main_full.nf.test.snap @@ -0,0 +1,49 @@ +{ + "-profile test_full": { + "content": [ + { + "MD5SUM": { + "md5sum": 9.5 + }, + "SHASUM": { + "sha256sum": 9.5 + }, + "Workflow": { + "nf-core/datasync": "v1.0dev" + } + }, + [ + "md5sum", + "md5sum/human_grch38_sequence.md5", + "md5sum/test_fastq.md5", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_datasync_software_mqc_versions.yml", + "shasum", + "shasum/human_grch38_sequence.sha256", + "shasum/test_fastq.sha256" + ], + [ + "human_grch38_sequence.md5:md5,4dd34e25c530b2c6e4637014711acc44", + "test_fastq.md5:md5,145df327e566f16b545fbca236f9bb62", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "human_grch38_sequence.sha256:md5,e3d6d2705970f75961eff5d5c09ce4d8", + "test_fastq.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-06-19T20:54:12.524244888" + } +} \ No newline at end of file From f628854a534a7347778a7f08f7d02bda77b5163e Mon Sep 17 00:00:00 2001 From: zxBIB Date: Fri, 19 Jun 2026 21:12:45 +0200 Subject: [PATCH 13/32] update default snapshot --- tests/default.nf.test.snap | 44 +++++++++++--------------------------- 1 file changed, 12 insertions(+), 32 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index a20e40d..b45596b 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -14,13 +14,8 @@ }, [ "md5sum", - "md5sum/GenomeSize.xml.md5", - "md5sum/GenomeSize.xml.old.md5", - "md5sum/genome.dict.md5", - "md5sum/genome.dict.old.md5", - "md5sum/genome.fa.fai.md5", - "md5sum/genome.fa.md5", - "md5sum/test2_1.fastq.gz.md5", + "md5sum/human_grch38_sequence.md5", + "md5sum/test_fastq.md5", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -34,36 +29,21 @@ "pipeline_info", "pipeline_info/nf_core_datasync_software_mqc_versions.yml", "shasum", - "shasum/GenomeSize.xml.old.sha256", - "shasum/GenomeSize.xml.sha256", - "shasum/genome.dict.old.sha256", - "shasum/genome.dict.sha256", - "shasum/genome.fa.fai.sha256", - "shasum/genome.fa.sha256", - "shasum/test2_1.fastq.gz.sha256" + "shasum/human_grch38_sequence.sha256", + "shasum/test_fastq.sha256" ], [ - "GenomeSize.xml.md5:md5,0c1c07f13ddcd6f479f8312b0c7d9843", - "GenomeSize.xml.old.md5:md5,8273ac6aa130edf9e628cf0cf2566855", - "genome.dict.md5:md5,cf34a65ce7a3e827c66eadb2d5522551", - "genome.dict.old.md5:md5,4dfbb85cd00197e03f43f999b39addab", - "genome.fa.fai.md5:md5,8fc26b8f3ce6b83f9860ae9a2347d046", - "genome.fa.md5:md5,cca9026fcc32a789c00d9070edac5809", - "test2_1.fastq.gz.md5:md5,145df327e566f16b545fbca236f9bb62", + "human_grch38_sequence.md5:md5,4dd34e25c530b2c6e4637014711acc44", + "test_fastq.md5:md5,145df327e566f16b545fbca236f9bb62", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "GenomeSize.xml.old.sha256:md5,068e91cdcc084710caf61a0859ac2be9", - "GenomeSize.xml.sha256:md5,e7a175f04cab11ce0a245133d70de9fb", - "genome.dict.old.sha256:md5,77492c77f911887b269de347e157d4ca", - "genome.dict.sha256:md5,0021eaba625d4dc9fcec55eb7384426e", - "genome.fa.fai.sha256:md5,99f227079c0fd354f272c0046482ff1a", - "genome.fa.sha256:md5,9bdb272c4b51342a0f139fbc14d0a57e", - "test2_1.fastq.gz.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" + "human_grch38_sequence.sha256:md5,e3d6d2705970f75961eff5d5c09ce4d8", + "test_fastq.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" ] ], - "timestamp": "2026-06-18T03:05:43.540206333", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.4" - } + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-06-19T21:05:19.976503457" } } \ No newline at end of file From 5444dd7b9f738f066a6dbc5acc059800d2ddca3d Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Mon, 22 Jun 2026 20:56:28 +0000 Subject: [PATCH 14/32] remove pipeline tag --- tests/main_full.nf.test | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/main_full.nf.test b/tests/main_full.nf.test index 47558e6..4d57d71 100644 --- a/tests/main_full.nf.test +++ b/tests/main_full.nf.test @@ -2,7 +2,6 @@ nextflow_pipeline { name "Test pipeline" script "../main.nf" - tag "pipeline" test("-profile test_full") { From 8c73c57419b3fd1566e949117ca656e1b8b15aaf Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Mon, 22 Jun 2026 20:57:06 +0000 Subject: [PATCH 15/32] fix: use test data base path param --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index af7be2f..770e4ff 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data for full size test // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = "https://raw.githubusercontent.com/nf-core/test-datasets/datasync/test-data/samplesheet.csv" + input = params.pipelines_testdata_base_path + "datasync/test-data/samplesheet.csv" // Genome references genome = 'R64-1-1' From 44499b95c4cc852fe5fd55f530dc34ac52813526 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:00:44 +0000 Subject: [PATCH 16/32] fix test_data base path --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 1b1ea2e..c383076 100644 --- a/nextflow.config +++ b/nextflow.config @@ -36,7 +36,7 @@ params { help_full = false show_hidden = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/datasync/' trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') // Config options From d4e0a4b9a42a1aa52c6906b531b46795f3fd94e1 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:00:57 +0000 Subject: [PATCH 17/32] remove debug print --- workflows/datasync.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/datasync.nf b/workflows/datasync.nf index a184b77..82d05b0 100644 --- a/workflows/datasync.nf +++ b/workflows/datasync.nf @@ -44,7 +44,6 @@ workflow DATASYNC { sha: !sha.isEmpty() return [ meta, sha ] } - MD5SUM( ch_samplesheet.input, false From 9ba6d19999acb2e41d6f6710c4d424305c63b804 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:01:13 +0000 Subject: [PATCH 18/32] update test_full test --- tests/main_full.nf.test | 1 + tests/main_full.nf.test.snap | 45 ++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 tests/main_full.nf.test.snap diff --git a/tests/main_full.nf.test b/tests/main_full.nf.test index 47558e6..640485d 100644 --- a/tests/main_full.nf.test +++ b/tests/main_full.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test pipeline" script "../main.nf" tag "pipeline" + profile "test_full" test("-profile test_full") { diff --git a/tests/main_full.nf.test.snap b/tests/main_full.nf.test.snap new file mode 100644 index 0000000..b8c1577 --- /dev/null +++ b/tests/main_full.nf.test.snap @@ -0,0 +1,45 @@ +{ + "-profile test_full": { + "content": [ + { + "MD5SUM": { + "md5sum": 9.5 + }, + "SHASUM": { + "sha256sum": 9.5 + }, + "Workflow": { + "nf-core/datasync": "v1.0dev" + } + }, + [ + "md5sum", + "md5sum/demultiplex.md5", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_datasync_software_mqc_versions.yml", + "shasum", + "shasum/demultiplex.sha256" + ], + [ + "demultiplex.md5:md5,d949186254af955f49ad9c8c0ea2a33c", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "demultiplex.sha256:md5,db74d30dff39da108b2f9dc0cdc90779" + ] + ], + "timestamp": "2026-06-23T15:41:43.847937556", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } + } +} \ No newline at end of file From a2922fe8451c60797e34415122e5f3892061c92c Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:01:27 +0000 Subject: [PATCH 19/32] make validation columns optional --- assets/schema_input.json | 4 ---- 1 file changed, 4 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 7dfd8d2..2a3472b 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -32,10 +32,6 @@ "required": [ "sample", "input" - ], - "anyOf": [ - { "required" : ["checksum_md5"] }, - { "required" : ["checksum_sha"] } ] } } From 00c6505f487d0b1e4a56e6ed690d44066880d5b0 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:01:46 +0000 Subject: [PATCH 20/32] fix samplesheet input path --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index af7be2f..b6ad8f0 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data for full size test // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = "https://raw.githubusercontent.com/nf-core/test-datasets/datasync/test-data/samplesheet.csv" + input = params.pipelines_testdata_base_path + "test-data/samplesheet.csv" // Genome references genome = 'R64-1-1' From f2114d4858f590b31fe7f22d019aef959ad6e65e Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:02:01 +0000 Subject: [PATCH 21/32] remove md5 test file --- assets/checksum.md5 | 21 --------------------- 1 file changed, 21 deletions(-) delete mode 100644 assets/checksum.md5 diff --git a/assets/checksum.md5 b/assets/checksum.md5 deleted file mode 100644 index b851672..0000000 --- a/assets/checksum.md5 +++ /dev/null @@ -1,21 +0,0 @@ -6cae999421b3107d31aaee312a67b2b4 BWAIndex/genome.fa.pac -dee21a414c8c9435c516ce51453eac69 BWAIndex/genome.fa.ann -a6da8681616c05eb542f1d91606a7b2f BWAIndex/genome.fa -6cae999421b3107d31aaee312a67b2b4 BWAIndex/version0.6.0/genome.fa.pac -dee21a414c8c9435c516ce51453eac69 BWAIndex/version0.6.0/genome.fa.ann -a6da8681616c05eb542f1d91606a7b2f BWAIndex/version0.6.0/genome.fa -b5666883af79e600563852fbd6db60ff BWAIndex/version0.6.0/genome.fa.sa -54d052dc82eee7a34465b8e8a8989631 BWAIndex/version0.6.0/genome.fa.amb -88712af9626d5cbba82007cf8e3f90b2 BWAIndex/version0.6.0/genome.fa.bwt -6cae999421b3107d31aaee312a67b2b4 BWAIndex/version0.5.x/genome.fa.pac -dee21a414c8c9435c516ce51453eac69 BWAIndex/version0.5.x/genome.fa.ann -a6da8681616c05eb542f1d91606a7b2f BWAIndex/version0.5.x/genome.fa -826ca9f3dd61da0e50e869ead26edd99 BWAIndex/version0.5.x/genome.fa.rpac -08b6a8da1dae3f4d22e2e78887ddc9e4 BWAIndex/version0.5.x/genome.fa.rsa -456ac470698ac3ce1bb56110f00ac732 BWAIndex/version0.5.x/genome.fa.sa -54d052dc82eee7a34465b8e8a8989631 BWAIndex/version0.5.x/genome.fa.amb -d48c35964b0817176190aab0c8270e5d BWAIndex/version0.5.x/genome.fa.rbwt -9177d5f8c71ec47f65ccf0ab189ab408 BWAIndex/version0.5.x/genome.fa.bwt -b5666883af79e600563852fbd6db60ff BWAIndex/genome.fa.sa -54d052dc82eee7a34465b8e8a8989631 BWAIndex/genome.fa.amb -88712af9626d5cbba82007cf8e3f90b2 BWAIndex/genome.fa.bwt From 7d62585022e78236e33519756cd269b56abb28f3 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:02:18 +0000 Subject: [PATCH 22/32] replace for original samplesheet --- assets/samplesheet.csv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index e4ef522..82e35fd 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,3 @@ -sample,input,checksum_md5 -human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/,assets/checksum.md5 -test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz,f06e81ce1eb2d5424f88ca7f345ec0d1 +sample,input +human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/ +test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz \ No newline at end of file From bff43f77774dc84fe082824e72fe11eb235619a9 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:22:58 +0000 Subject: [PATCH 23/32] update default snapshot --- tests/default.nf.test.snap | 38 +++++++++----------------------------- 1 file changed, 9 insertions(+), 29 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index a20e40d..5ac94b6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -14,13 +14,8 @@ }, [ "md5sum", - "md5sum/GenomeSize.xml.md5", - "md5sum/GenomeSize.xml.old.md5", - "md5sum/genome.dict.md5", - "md5sum/genome.dict.old.md5", - "md5sum/genome.fa.fai.md5", - "md5sum/genome.fa.md5", - "md5sum/test2_1.fastq.gz.md5", + "md5sum/human_grch38_sequence.md5", + "md5sum/test_fastq.md5", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -34,33 +29,18 @@ "pipeline_info", "pipeline_info/nf_core_datasync_software_mqc_versions.yml", "shasum", - "shasum/GenomeSize.xml.old.sha256", - "shasum/GenomeSize.xml.sha256", - "shasum/genome.dict.old.sha256", - "shasum/genome.dict.sha256", - "shasum/genome.fa.fai.sha256", - "shasum/genome.fa.sha256", - "shasum/test2_1.fastq.gz.sha256" + "shasum/human_grch38_sequence.sha256", + "shasum/test_fastq.sha256" ], [ - "GenomeSize.xml.md5:md5,0c1c07f13ddcd6f479f8312b0c7d9843", - "GenomeSize.xml.old.md5:md5,8273ac6aa130edf9e628cf0cf2566855", - "genome.dict.md5:md5,cf34a65ce7a3e827c66eadb2d5522551", - "genome.dict.old.md5:md5,4dfbb85cd00197e03f43f999b39addab", - "genome.fa.fai.md5:md5,8fc26b8f3ce6b83f9860ae9a2347d046", - "genome.fa.md5:md5,cca9026fcc32a789c00d9070edac5809", - "test2_1.fastq.gz.md5:md5,145df327e566f16b545fbca236f9bb62", + "human_grch38_sequence.md5:md5,9a8b3f1bfffd9f0d4ff90c03851dae64", + "test_fastq.md5:md5,145df327e566f16b545fbca236f9bb62", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "GenomeSize.xml.old.sha256:md5,068e91cdcc084710caf61a0859ac2be9", - "GenomeSize.xml.sha256:md5,e7a175f04cab11ce0a245133d70de9fb", - "genome.dict.old.sha256:md5,77492c77f911887b269de347e157d4ca", - "genome.dict.sha256:md5,0021eaba625d4dc9fcec55eb7384426e", - "genome.fa.fai.sha256:md5,99f227079c0fd354f272c0046482ff1a", - "genome.fa.sha256:md5,9bdb272c4b51342a0f139fbc14d0a57e", - "test2_1.fastq.gz.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" + "human_grch38_sequence.sha256:md5,809eee5059df78f56a9201ef1af8367b", + "test_fastq.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" ] ], - "timestamp": "2026-06-18T03:05:43.540206333", + "timestamp": "2026-06-23T16:22:23.074516015", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" From e6ce004840dfc8aa3463ae978a2b34856c2f32c7 Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:44:49 +0000 Subject: [PATCH 24/32] run pre commit --- assets/samplesheet.csv | 2 +- assets/schema_input.json | 5 +---- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 82e35fd..55cd8f9 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,3 @@ sample,input human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/ -test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz \ No newline at end of file +test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz diff --git a/assets/schema_input.json b/assets/schema_input.json index 2a3472b..b2c4ddf 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -29,9 +29,6 @@ "errorMessage": "Checksum_sha cannot contain spaces" } }, - "required": [ - "sample", - "input" - ] + "required": ["sample", "input"] } } From 68e00d2dec7cbb4d87a6e39d861d8b47111f82df Mon Sep 17 00:00:00 2001 From: Maria Antonia Saracco Date: Tue, 23 Jun 2026 16:57:17 +0000 Subject: [PATCH 25/32] update default snapshot --- tests/default.nf.test.snap | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e7ca513..0ef2a23 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -16,8 +16,6 @@ "md5sum", "md5sum/human_grch38_sequence.md5", "md5sum/test_fastq.md5", - "md5sum/human_grch38_sequence.md5", - "md5sum/test_fastq.md5", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -33,8 +31,6 @@ "shasum", "shasum/human_grch38_sequence.sha256", "shasum/test_fastq.sha256" - "shasum/human_grch38_sequence.sha256", - "shasum/test_fastq.sha256" ], [ "human_grch38_sequence.md5:md5,9a8b3f1bfffd9f0d4ff90c03851dae64", @@ -44,11 +40,10 @@ "test_fastq.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" ] ], - "timestamp": "2026-06-23T16:22:23.074516015", + "timestamp": "2026-06-23T16:56:56.622054559", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-06-19T21:05:19.976503457" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file From 24acf68ab5427eaacf4570746023f4e17088bd3d Mon Sep 17 00:00:00 2001 From: Antonia Saracco Date: Tue, 23 Jun 2026 17:46:02 +0000 Subject: [PATCH 26/32] update test data base paht in schema --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 10b92c1..75bee3d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -208,7 +208,7 @@ "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/datasync/", "hidden": true }, "trace_report_suffix": { From 128044cb49d65034364a18bfe7517288095c3b84 Mon Sep 17 00:00:00 2001 From: Antonia Saracco Date: Tue, 23 Jun 2026 17:46:14 +0000 Subject: [PATCH 27/32] update snapshot --- tests/main_full.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/main_full.nf.test.snap b/tests/main_full.nf.test.snap index b8c1577..d308a81 100644 --- a/tests/main_full.nf.test.snap +++ b/tests/main_full.nf.test.snap @@ -31,15 +31,15 @@ "shasum/demultiplex.sha256" ], [ - "demultiplex.md5:md5,d949186254af955f49ad9c8c0ea2a33c", + "demultiplex.md5:md5,ab5b41890200d7aed339157e7a898667", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "demultiplex.sha256:md5,db74d30dff39da108b2f9dc0cdc90779" + "demultiplex.sha256:md5,ee93070f17fc2392309c9b411958ca76" ] ], - "timestamp": "2026-06-23T15:41:43.847937556", + "timestamp": "2026-06-23T17:43:27.311534744", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.4" + "nextflow": "25.10.4" } } } \ No newline at end of file From f02371fee942085d70eeed2da5eaf8d0a0680bef Mon Sep 17 00:00:00 2001 From: Antonia Saracco Date: Tue, 23 Jun 2026 17:54:21 +0000 Subject: [PATCH 28/32] update default snapshot --- tests/default.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0ef2a23..1476e51 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -33,17 +33,17 @@ "shasum/test_fastq.sha256" ], [ - "human_grch38_sequence.md5:md5,9a8b3f1bfffd9f0d4ff90c03851dae64", + "human_grch38_sequence.md5:md5,5bfe720bd56b2849fe80c5f4e19b828d", "test_fastq.md5:md5,145df327e566f16b545fbca236f9bb62", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "human_grch38_sequence.sha256:md5,809eee5059df78f56a9201ef1af8367b", + "human_grch38_sequence.sha256:md5,977284c71f44223095224aba476805eb", "test_fastq.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" ] ], - "timestamp": "2026-06-23T16:56:56.622054559", + "timestamp": "2026-06-23T17:52:29.444424755", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.4" + "nextflow": "25.10.4" } } } \ No newline at end of file From 0b468d0d3668c7c5f97edbb73f748fbe4502a626 Mon Sep 17 00:00:00 2001 From: Antonia Saracco Date: Tue, 23 Jun 2026 19:33:56 +0000 Subject: [PATCH 29/32] ignore md5 and sha unstable results --- tests/.nftignore | 2 ++ tests/default.nf.test.snap | 8 ++------ tests/main_full.nf.test.snap | 6 ++---- 3 files changed, 6 insertions(+), 10 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index e128a12..912a033 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -10,3 +10,5 @@ multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html fastqc/*_fastqc.{html,zip} pipeline_info/*.{html,json,txt,yml} +md5sum/** +shasum/** \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1476e51..2c00759 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -33,14 +33,10 @@ "shasum/test_fastq.sha256" ], [ - "human_grch38_sequence.md5:md5,5bfe720bd56b2849fe80c5f4e19b828d", - "test_fastq.md5:md5,145df327e566f16b545fbca236f9bb62", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "human_grch38_sequence.sha256:md5,977284c71f44223095224aba476805eb", - "test_fastq.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f" + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-06-23T17:52:29.444424755", + "timestamp": "2026-06-23T19:18:17.852339994", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/main_full.nf.test.snap b/tests/main_full.nf.test.snap index d308a81..0f54dbb 100644 --- a/tests/main_full.nf.test.snap +++ b/tests/main_full.nf.test.snap @@ -31,12 +31,10 @@ "shasum/demultiplex.sha256" ], [ - "demultiplex.md5:md5,ab5b41890200d7aed339157e7a898667", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "demultiplex.sha256:md5,ee93070f17fc2392309c9b411958ca76" + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-06-23T17:43:27.311534744", + "timestamp": "2026-06-23T19:32:18.469702006", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 8a3e5d634a2d38891e87cd0514f212d2a4fef10e Mon Sep 17 00:00:00 2001 From: Antonia Saracco Date: Tue, 23 Jun 2026 19:36:18 +0000 Subject: [PATCH 30/32] fix: add new line at the end of file --- tests/.nftignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/.nftignore b/tests/.nftignore index 912a033..18b80cb 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -11,4 +11,4 @@ multiqc/multiqc_report.html fastqc/*_fastqc.{html,zip} pipeline_info/*.{html,json,txt,yml} md5sum/** -shasum/** \ No newline at end of file +shasum/** From 27e038ce0a274c43c0d54971229d50db50f20152 Mon Sep 17 00:00:00 2001 From: Antonia Saracco Date: Tue, 23 Jun 2026 19:57:25 +0000 Subject: [PATCH 31/32] update shasum module --- modules.json | 2 +- modules/nf-core/shasum/main.nf | 38 +++++++++++++---- modules/nf-core/shasum/meta.yml | 9 +++- modules/nf-core/shasum/tests/main.nf.test | 33 ++++++++++++++- .../nf-core/shasum/tests/main.nf.test.snap | 42 ++++++++++++++++--- 5 files changed, 104 insertions(+), 20 deletions(-) diff --git a/modules.json b/modules.json index a6c41ad..711f257 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "shasum": { "branch": "master", - "git_sha": "ef2ee0358c7d03231834aeac816991aeb20debd7", + "git_sha": "429d56ab5b5879549f71bf9905104f39d0c3bff4", "installed_by": ["modules"] } } diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index b79d387..65dffad 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -9,6 +9,7 @@ process SHASUM { input: tuple val(meta), path(files) + val as_separate_files output: tuple val(meta), path("*.sha256"), emit: checksum @@ -20,16 +21,35 @@ process SHASUM { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - """ - find -L * -type f \\ - ! -name '*.sha256' \\ - -exec sha256sum ${args} "{}" + \\ - > ${prefix}.sha256 - """ + // will only use when as_separate_files = false + if (as_separate_files) { + """ + find -L * -maxdepth 0 -type f \\ + ! -name '*.sha256' \\ + -exec sh -c 'sha256sum ${args} "\$1" > "\$1.sha256"' _ "{}" \\; + """ + } + else { + """ + find -L * -type f \\ + ! -name '*.sha256' \\ + -exec sha256sum ${args} "{}" + \\ + > ${prefix}.sha256 + """ + } stub: def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.sha256 - """ + if (as_separate_files) { + """ + find -L * -type f \\ + ! -name '*.sha256' \\ + -exec sh -c 'touch "\$1.sha256"' _ "{}" \\; + """ + } + else { + """ + touch ${prefix}.sha256 + """ + } } diff --git a/modules/nf-core/shasum/meta.yml b/modules/nf-core/shasum/meta.yml index 327a4f0..e4b7648 100644 --- a/modules/nf-core/shasum/meta.yml +++ b/modules/nf-core/shasum/meta.yml @@ -18,11 +18,16 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - file: + - files: type: file - description: Any file + description: Any number of files pattern: "*.*" ontologies: [] + - as_separate_files: + type: boolean + description: | + If true, each file will have its own shasum file. If false, all files will be + checksummed into a single shasum file. output: checksum: - - meta: diff --git a/modules/nf-core/shasum/tests/main.nf.test b/modules/nf-core/shasum/tests/main.nf.test index 02d2ac0..6e2d413 100644 --- a/modules/nf-core/shasum/tests/main.nf.test +++ b/modules/nf-core/shasum/tests/main.nf.test @@ -9,16 +9,44 @@ nextflow_process { tag "modules_nfcore" tag "shasum" - test("test-shasum") { + test("test-shasum, separate") { when { process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] ] + input[1] = true + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-shasum, combined") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[1] = false """ } } @@ -42,6 +70,7 @@ nextflow_process { [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] + input[1] = true """ } diff --git a/modules/nf-core/shasum/tests/main.nf.test.snap b/modules/nf-core/shasum/tests/main.nf.test.snap index a86583b..df3986f 100644 --- a/modules/nf-core/shasum/tests/main.nf.test.snap +++ b/modules/nf-core/shasum/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test-shasum": { + "test-shasum, combined": { "content": [ { "checksum": [ @@ -8,7 +8,7 @@ "id": "test", "single_end": false }, - "test.paired_end.bam.sha256:md5,138a19e100f09fc975ea1b717da9b6dd" + "test.sha256:md5,cbe368d92c146935e6d72a00c2c2c804" ] ], "versions_sha256sum": [ @@ -20,10 +20,10 @@ ] } ], - "timestamp": "2026-05-03T20:43:40.688253838", + "timestamp": "2026-06-19T13:40:52.588704139", "meta": { "nf-test": "0.9.5", - "nextflow": "24.10.4" + "nextflow": "26.04.4" } }, "test-shasum - stub": { @@ -47,10 +47,40 @@ ] } ], - "timestamp": "2026-05-03T20:43:46.125782074", + "timestamp": "2026-06-19T13:40:59.232985121", "meta": { "nf-test": "0.9.5", - "nextflow": "24.10.4" + "nextflow": "26.04.4" + } + }, + "test-shasum, separate": { + "content": [ + { + "checksum": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastq.gz.sha256:md5,d200e9d01dfc874b9c5efe894181b430", + "test_2.fastq.gz.sha256:md5,0035d52e9b642206858b826f2b49d7a3" + ] + ] + ], + "versions_sha256sum": [ + [ + "SHASUM", + "sha256sum", + "9.5" + ] + ] + } + ], + "timestamp": "2026-06-19T13:40:45.551657784", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.4" } } } \ No newline at end of file From dd9afc4442e0b43b6a7e1209ef2f4a20a36c233c Mon Sep 17 00:00:00 2001 From: Antonia Saracco Date: Tue, 23 Jun 2026 20:04:06 +0000 Subject: [PATCH 32/32] fix: update shasum input --- workflows/datasync.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/datasync.nf b/workflows/datasync.nf index 82d05b0..cb4d985 100644 --- a/workflows/datasync.nf +++ b/workflows/datasync.nf @@ -50,7 +50,8 @@ workflow DATASYNC { ) SHASUM( - ch_samplesheet.input + ch_samplesheet.input, + false ) //