From 514ec119a665ad7f8546fffe14dd4d1af6f7d32e Mon Sep 17 00:00:00 2001 From: EliseCos Date: Wed, 3 Jun 2026 18:21:39 +0200 Subject: [PATCH 1/6] [WIP] Add FD --- assets/multiqc_config.yml | 21 ++++++++++++++++----- conf/base.config | 6 +++--- main.nf | 1 + modules/local/preproc/singleeddy/main.nf | 14 +++++++++----- 4 files changed, 29 insertions(+), 13 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c43e173..015a048 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -7,14 +7,19 @@ report_section_order: order: -200 pre_qc_sampling_mqc: order: -300 - registration_qc: + framewise_displacement: order: -500 - dti_qc: + registration_qc: order: -600 + dti_qc: + order: -700 tracking_mask_qc: - order: -700 + order: -800 tracking_qc: - order: -800 + order: -900 + +modules_order: + - framewise_displacement custom_data: pre_qc_rgb: @@ -89,4 +94,10 @@ sp: tracking_mask_qc: fn: "*_mask_tracking_mqc.png" tracking_qc: - fn: "*local_tracking_mqc.png" \ No newline at end of file + fn: "*local_tracking_mqc.png" + +# Customisable module parameters +framewise_displacement: + warn_threshold: 0.05 + fail_threshold: 0.12 + unit: "µm" \ No newline at end of file diff --git a/conf/base.config b/conf/base.config index aeea44f..43fe1ec 100644 --- a/conf/base.config +++ b/conf/base.config @@ -36,9 +36,9 @@ process { time = { 8.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } } withLabel:process_high { - cpus = { 10 * task.attempt * (executor.name == 'slurm' ? 2 : 1) } - memory = { 14.GB * task.attempt * (executor.name == 'slurm' ? 2 : 1) } - time = { 16.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } + cpus = { 4 * task.attempt * (executor.name == 'slurm' ? 2 : 1) } + memory = { 8.GB * task.attempt * (executor.name == 'slurm' ? 2 : 1) } + time = { 8.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } } withLabel:process_long { time = { 20.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } diff --git a/main.nf b/main.nf index 00e34a5..521bb4e 100644 --- a/main.nf +++ b/main.nf @@ -145,6 +145,7 @@ workflow { ch_after_eddy = PREPROC_SINGLEEDDY.out.dwi_corrected.join( PREPROC_SINGLEEDDY.out.bval_corrected).join( PREPROC_SINGLEEDDY.out.bvec_corrected) + ch_multiqc_files = ch_multiqc_files.mix(PREPROC_SINGLEEDDY.out.eddy_fd_mqc) } else { ch_after_eddy = ch_eddy diff --git a/modules/local/preproc/singleeddy/main.nf b/modules/local/preproc/singleeddy/main.nf index 40ef8bb..129691c 100644 --- a/modules/local/preproc/singleeddy/main.nf +++ b/modules/local/preproc/singleeddy/main.nf @@ -7,10 +7,11 @@ process PREPROC_SINGLEEDDY { input: tuple val(meta), path(dwi), path(bval), path(bvec) output: - tuple val(meta), path("*__dwi_eddy_corrected.nii.gz") , emit: dwi_corrected - tuple val(meta), path("*__dwi_eddy_corrected.bval") , emit: bval_corrected - tuple val(meta), path("*__dwi_eddy_corrected.bvec") , emit: bvec_corrected - path "versions.yml" , emit: versions + tuple val(meta), path("*__dwi_eddy_corrected.nii.gz") , emit: dwi_corrected + tuple val(meta), path("*__dwi_eddy_corrected.bval") , emit: bval_corrected + tuple val(meta), path("*__dwi_eddy_corrected.bvec") , emit: bvec_corrected + tuple val(meta), path("*__dwi_eddy_restricted_movement_rms.txt") , emit: eddy_fd_mqc, optional:true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -42,9 +43,11 @@ process PREPROC_SINGLEEDDY { echo "--nthr=$extra_thr --very_verbose $extra_args --niter=$extra_ite" >> eddy.sh sh eddy.sh - mv ${prefix}__.nii.gz ${prefix}__dwi_eddy_corrected.nii.gz + mv ${prefix}__.nii.gz ${prefix}__dwi_eddy_corrected.nii.gz mv ${prefix}__.eddy_rotated_bvecs ${prefix}__dwi_eddy_corrected.bvec mv ${bval} ${prefix}__dwi_eddy_corrected.bval + mv ${prefix}__dwi_eddy_corrected.eddy_restricted_movement_rms ${prefix}__dwi_eddy_restricted_movement_rms.txt + cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -63,6 +66,7 @@ process PREPROC_SINGLEEDDY { touch ${prefix}__dwi_eddy_corrected.nii.gz touch ${prefix}__dwi_eddy_corrected.bval touch ${prefix}__dwi_eddy_corrected.bvec + touch ${prefix}__dwi_eddy_restricted_movement_rms.txt cat <<-END_VERSIONS > versions.yml "${task.process}": From dd660714fac085dd6f49f34289252968a5d58d14 Mon Sep 17 00:00:00 2001 From: EliseCos Date: Wed, 3 Jun 2026 18:32:50 +0200 Subject: [PATCH 2/6] [ENH] update multiqc module --- modules.json | 2 +- .../linux_amd64-bd-c17fb751507e9dfc_1.txt | 1526 +++++++++++++++++ .../linux_arm64-bd-5c84a5000a226ab5_1.txt | 1476 ++++++++++++++++ modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 53 +- modules/nf-core/multiqc/meta.yml | 165 +- .../multiqc/tests/custom_prefix.config | 5 + modules/nf-core/multiqc/tests/main.nf.test | 191 ++- .../nf-core/multiqc/tests/main.nf.test.snap | 435 ++++- modules/nf-core/multiqc/tests/nextflow.config | 1 + 10 files changed, 3696 insertions(+), 160 deletions(-) create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt create mode 100644 modules/nf-core/multiqc/tests/custom_prefix.config diff --git a/modules.json b/modules.json index 9a9155e..14c366e 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] } } diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt new file mode 100644 index 0000000..2a91c22 --- /dev/null +++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt @@ -0,0 +1,1526 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: 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a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 5cb7162..c4bc715 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,63 +1,50 @@ process MULTIQC { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ 'multiqc/multiqc:v1.31' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: - tuple val(meta), path(qc_images) // Added input with subject meta field. - path multiqc_files - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - path(replace_names) - path(sample_names) + tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions + tuple val(meta), path("*.html"), emit: report + tuple val(meta), path("*_data"), emit: data + tuple val(meta), path("*_plots"), emit: plots, optional: true + // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever + tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = "--filename ${meta.id}_multiqc_report" - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' + def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : "" def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' def replace = replace_names ? "--replace-names ${replace_names}" : '' def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ - $args \\ - $config \\ - $prefix \\ - $extra_config \\ - $logo \\ - $replace \\ - $samples \\ + ${args} \\ + ${config} \\ + ${prefix} \\ + ${logo} \\ + ${replace} \\ + ${samples} \\ . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ stub: """ mkdir multiqc_data + touch multiqc_data/.stub mkdir multiqc_plots + touch multiqc_plots/.stub touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ce30eb7..27ce18d 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,6 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into - a single report +description: Aggregate results from bioinformatics analyses across many samples + into a single report keywords: - QC - bioinformatics tools @@ -12,74 +12,91 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - ontologies: [] - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - ontologies: [] - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV -output: - report: - - "*multiqc_report.html": + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - multiqc_files: type: file - description: MultiQC report file - pattern: "multiqc_report.html" + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC ontologies: [] - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - plots: - - "*_plots": + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 + - multiqc_logo: type: file - description: Plots created by MultiQC - pattern: "*_data" + description: Optional logo file for MultiQC + pattern: "*.{png}" ontologies: [] - versions: - - versions.yml: + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 + - sample_names: type: file - description: File containing software versions - pattern: "versions.yml" + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - edam: http://edamontology.org/format_3475 +output: + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*.html": + type: file + description: MultiQC report file + pattern: ".html" + ontologies: [] + data: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_plots" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g": + type: eval + description: The expression to obtain the version of the tool authors: - "@abhi18av" - "@bunop" @@ -90,3 +107,27 @@ maintainers: - "@bunop" - "@drpatelh" - "@jfy133" +containers: + conda: + linux/amd64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt + linux/arm64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt + docker: + linux/amd64: + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 + linux/arm64: + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data + linux/arm64: + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config new file mode 100644 index 0000000..b30b135 --- /dev/null +++ b/modules/nf-core/multiqc/tests/custom_prefix.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = "custom_prefix" + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7..4cbdb95 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -15,25 +15,84 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] - custom prefix") { + config "./custom_prefix.config" + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) + """ + } } + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } } test("sarscov2 single-end [fastqc] [config]") { @@ -41,23 +100,85 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] [multiple configs]") { + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [ + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true) + ], + [], + [], + [] + ]) + """ + } + } + + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -68,25 +189,23 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 17881d1..4489921 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,41 +1,422 @@ { - "multiqc_versions_single": { + "sarscov2 single-end [fastqc] [multiple configs]": { "content": [ - [ - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-03-17T16:15:42.577775492", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-08T20:57:36.139055243" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_stub": { + "sarscov2 single-end [fastqc]": { "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-03-17T16:21:17.072841555", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-08T20:59:15.142230631" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_versions_config": { + "sarscov2 single-end [fastqc] - stub": { "content": [ - [ - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" - ] + { + "data": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "plots": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "report": [ + [ + { + "id": "FASTQC" + }, + "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-02-26T15:14:39.789193051", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-08T20:58:29.629087066" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] [config]": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:30.372239611", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] - custom prefix": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "custom_prefix.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:18.189023981", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config index c537a6a..374dfef 100644 --- a/modules/nf-core/multiqc/tests/nextflow.config +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -1,5 +1,6 @@ process { withName: 'MULTIQC' { ext.prefix = null + ext.args = '-p' } } From c8e632c3271d2c7e6992b43d6416a12ee57d0bac Mon Sep 17 00:00:00 2001 From: EliseCos Date: Thu, 4 Jun 2026 08:59:33 +0000 Subject: [PATCH 3/6] [WIP] fix + restore qc --- modules/local/preproc/singleeddy/main.nf | 2 +- modules/nf-core/multiqc/main.nf | 55 +++++++++++++++--------- 2 files changed, 35 insertions(+), 22 deletions(-) diff --git a/modules/local/preproc/singleeddy/main.nf b/modules/local/preproc/singleeddy/main.nf index 129691c..37d9c04 100644 --- a/modules/local/preproc/singleeddy/main.nf +++ b/modules/local/preproc/singleeddy/main.nf @@ -46,7 +46,7 @@ process PREPROC_SINGLEEDDY { mv ${prefix}__.nii.gz ${prefix}__dwi_eddy_corrected.nii.gz mv ${prefix}__.eddy_rotated_bvecs ${prefix}__dwi_eddy_corrected.bvec mv ${bval} ${prefix}__dwi_eddy_corrected.bval - mv ${prefix}__dwi_eddy_corrected.eddy_restricted_movement_rms ${prefix}__dwi_eddy_restricted_movement_rms.txt + mv ${prefix}__.eddy_restricted_movement_rms ${prefix}__dwi_eddy_restricted_movement_rms.txt cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index c4bc715..649898c 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,50 +1,63 @@ process MULTIQC { - tag "${meta.id}" + tag "$meta.id" label 'process_single' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' - : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" + container "${ 'multiqc/multiqc:v1.31' }" input: - tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) + tuple val(meta), path(qc_images) // Added input with subject meta field. + path multiqc_files + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) + path(replace_names) + path(sample_names) output: - tuple val(meta), path("*.html"), emit: report - tuple val(meta), path("*_data"), emit: data - tuple val(meta), path("*_plots"), emit: plots, optional: true - // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever - tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' - def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : "" + def prefix = "--filename ${meta.id}_multiqc_report" + def config = multiqc_config ? "--config $multiqc_config" : '' + def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' def replace = replace_names ? "--replace-names ${replace_names}" : '' def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ - ${args} \\ - ${config} \\ - ${prefix} \\ - ${logo} \\ - ${replace} \\ - ${samples} \\ + $args \\ + $config \\ + $prefix \\ + $extra_config \\ + $logo \\ + $replace \\ + $samples \\ . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS """ stub: """ mkdir multiqc_data - touch multiqc_data/.stub mkdir multiqc_plots - touch multiqc_plots/.stub touch multiqc_report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS """ -} +} \ No newline at end of file From 2c47da6219c593f7cd870743f8d35acfc8dea20d Mon Sep 17 00:00:00 2001 From: EliseCos Date: Fri, 5 Jun 2026 12:16:48 +0000 Subject: [PATCH 4/6] [ENH] add plot FD in QC --- assets/multiqc_config.yml | 14 +++++++++----- modules/local/preproc/singleeddy/meta.yml | 9 +++++++++ modules/nf-core/multiqc/main.nf | 5 ++++- modules/nf-core/multiqc/meta.yml | 6 ++++++ 4 files changed, 28 insertions(+), 6 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 015a048..2e65d85 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,11 +3,11 @@ report_comment: > analysis pipeline. report_section_order: - pre_qc_rgb: + framewise_displacement: order: -200 - pre_qc_sampling_mqc: + pre_qc_rgb: order: -300 - framewise_displacement: + pre_qc_sampling_mqc: order: -500 registration_qc: order: -600 @@ -18,7 +18,7 @@ report_section_order: tracking_qc: order: -900 -modules_order: +module_order: - framewise_displacement custom_data: @@ -83,6 +83,8 @@ custom_data: plot_type: "image" sp: + framewise_displacement: + fn: "*dwi_eddy_restricted_movement_rms.txt" pre_qc_rgb: fn: "*rgb_mqc.png" pre_qc_sampling_mqc: @@ -100,4 +102,6 @@ sp: framewise_displacement: warn_threshold: 0.05 fail_threshold: 0.12 - unit: "µm" \ No newline at end of file + unit: "µm" + +export_plots: true \ No newline at end of file diff --git a/modules/local/preproc/singleeddy/meta.yml b/modules/local/preproc/singleeddy/meta.yml index 73170dd..9a469b5 100755 --- a/modules/local/preproc/singleeddy/meta.yml +++ b/modules/local/preproc/singleeddy/meta.yml @@ -62,6 +62,15 @@ output: description: B-vectors corrected in FSL format pattern: "*__dwi_eddy_corrected.bvec" + - eddy_fd_mqc: + - "*__dwi_eddy_restricted_movement_rms.txt": + type: file + description: | + Text file containing framewise displacement (restricted movement) + information from eddy. Made for use in MultiQC report. + pattern: "*__dwi_eddy_restricted_movement_rms.txt" + ontologies: [] + - versions: type: file description: File containing software versions diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 649898c..a978607 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,7 +3,9 @@ process MULTIQC { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ 'multiqc/multiqc:v1.31' }" + container "gagnonanthony/multiqc-neuroimaging:0.1.0" + containerOptions((workflow.containerEngine == 'docker') ? '--entrypoint "" --user $(id -u):$(id -g)' : '') + input: tuple val(meta), path(qc_images) // Added input with subject meta field. @@ -58,6 +60,7 @@ process MULTIQC { cat <<-END_VERSIONS > versions.yml "${task.process}": multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + neuroimaging: \$( pip list | grep neuroimaging | awk '{print \$2}' ) END_VERSIONS """ } \ No newline at end of file diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 27ce18d..39d23ec 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -15,6 +15,12 @@ tools: licence: - "GPL-3.0-or-later" identifier: biotools:multiqc + - neuroimaging: + description: | + Neuroimaging is a python MultiQC plugin containing various tools for generating QC reports for neuroimaging data. + homepage: https://github.com/nf-neuro/MultiQC_neuroimaging + licence: ["MIT"] + identifier: "" input: - - meta: type: map From 4ec33cfb65279e7bbed30c52448a4ff10410648d Mon Sep 17 00:00:00 2001 From: EliseCos Date: Fri, 5 Jun 2026 12:24:29 +0000 Subject: [PATCH 5/6] restore base.config --- conf/base.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/base.config b/conf/base.config index 43fe1ec..aeea44f 100644 --- a/conf/base.config +++ b/conf/base.config @@ -36,9 +36,9 @@ process { time = { 8.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } } withLabel:process_high { - cpus = { 4 * task.attempt * (executor.name == 'slurm' ? 2 : 1) } - memory = { 8.GB * task.attempt * (executor.name == 'slurm' ? 2 : 1) } - time = { 8.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } + cpus = { 10 * task.attempt * (executor.name == 'slurm' ? 2 : 1) } + memory = { 14.GB * task.attempt * (executor.name == 'slurm' ? 2 : 1) } + time = { 16.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } } withLabel:process_long { time = { 20.h * task.attempt * (executor.name == 'slurm' ? 2 : 1) } From a281e99b05319595cb08ad0e32029c859d1e557c Mon Sep 17 00:00:00 2001 From: EliseCos Date: Wed, 17 Jun 2026 18:00:27 +0000 Subject: [PATCH 6/6] add channel mask for nnunet --- main.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 521bb4e..59523b0 100644 --- a/main.nf +++ b/main.nf @@ -161,8 +161,9 @@ workflow { } else { ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0) - .map { meta, dwi, bval, bvec, b0 -> - [meta, dwi, bval, b0 ?: [ ]]} + .join(data.mask, by: 0, remainder: true) + .map { meta, dwi, bval, bvec, b0, mask -> + [meta, dwi, bval, b0, mask ?: [ ]]} NNUNET(ch_nnunet)