[2025-09-19 10:56:40,253] git.util [DEBUG ] sys.platform='darwin', git_executable='git' [2025-09-19 10:56:40,254] git.util [DEBUG ] sys.platform='darwin', git_executable='git' [2025-09-19 10:56:40,254] git.cmd [DEBUG ] Popen(['git', 'version'], cwd=/Users/matthias.zepper/Documents/Coding/Nextflow/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) [2025-09-19 10:56:40,266] git.cmd [DEBUG ] Popen(['git', 'clone', '-v', '--progress', '--', 'https://github.com/nf-core/modules.git', '/Users/matthias.zepper/.config/nfcore/nf-core/modules'], cwd=/Users/matthias.zepper/Documents/Coding/Nextflow/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=True) [2025-09-19 10:56:48,760] git.util [DEBUG ] sys.platform='darwin', git_executable='git' [2025-09-19 10:56:48,761] git.util [DEBUG ] sys.platform='darwin', git_executable='git' [2025-09-19 10:56:48,763] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/Users/matthias.zepper/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-09-19 10:56:48,955] nf_core.utils [DEBUG ] Got '/Users/matthias.zepper/.config/nfcore/nf-core/modules' as path [2025-09-19 10:56:48,956] nf_core.utils [DEBUG ] No config cache found [2025-09-19 10:56:48,957] nf_core.utils [DEBUG ] Running command: nextflow config -flat /Users/matthias.zepper/.config/nfcore/nf-core/modules [2025-09-19 10:56:50,286] nf_core.utils [DEBUG ] Config key: params.input, value: null [2025-09-19 10:56:50,287] nf_core.utils [DEBUG ] Config key: params.multiqc_config, value: null [2025-09-19 10:56:50,287] nf_core.utils [DEBUG ] Config key: params.multiqc_title, value: null [2025-09-19 10:56:50,287] nf_core.utils [DEBUG ] Config key: params.multiqc_logo, value: null [2025-09-19 10:56:50,288] nf_core.utils [DEBUG ] Config key: params.max_multiqc_email_size, value: 25.MB [2025-09-19 10:56:50,288] nf_core.utils [DEBUG ] Config key: params.multiqc_methods_description, value: null [2025-09-19 10:56:50,288] nf_core.utils [DEBUG ] Config key: params.outdir, value: null [2025-09-19 10:56:50,289] nf_core.utils [DEBUG ] Config key: params.publish_dir_mode, value: copy [2025-09-19 10:56:50,289] nf_core.utils [DEBUG ] Config key: params.email, value: null [2025-09-19 10:56:50,289] nf_core.utils [DEBUG ] Config key: params.email_on_fail, value: null [2025-09-19 10:56:50,290] nf_core.utils [DEBUG ] Config key: params.plaintext_email, value: false [2025-09-19 10:56:50,290] nf_core.utils [DEBUG ] Config key: params.monochrome_logs, value: false [2025-09-19 10:56:50,290] nf_core.utils [DEBUG ] Config key: params.hook_url, value: null [2025-09-19 10:56:50,291] nf_core.utils [DEBUG ] Config key: params.help, value: false [2025-09-19 10:56:50,291] nf_core.utils [DEBUG ] Config key: params.help_full, value: false [2025-09-19 10:56:50,291] nf_core.utils [DEBUG ] Config key: params.show_hidden, value: false [2025-09-19 10:56:50,292] nf_core.utils [DEBUG ] Config key: params.version, value: false [2025-09-19 10:56:50,292] nf_core.utils [DEBUG ] Config key: params.pipelines_testdata_base_path, value: https://raw.githubusercontent.com/nf-core/test-datasets/ [2025-09-19 10:56:50,292] nf_core.utils [DEBUG ] Config key: params.trace_report_suffix, value: 2025-09-19_10-56-49 [2025-09-19 10:56:50,293] nf_core.utils [DEBUG ] Config key: params.config_profile_name, value: null [2025-09-19 10:56:50,293] nf_core.utils [DEBUG ] Config key: params.config_profile_description, value: null [2025-09-19 10:56:50,294] nf_core.utils [DEBUG ] Config key: params.custom_config_version, value: master [2025-09-19 10:56:50,294] nf_core.utils [DEBUG ] Config key: params.custom_config_base, value: https://raw.githubusercontent.com/nf-core/configs/master [2025-09-19 10:56:50,294] nf_core.utils [DEBUG ] Config key: params.config_profile_contact, value: null [2025-09-19 10:56:50,295] nf_core.utils [DEBUG ] Config key: params.config_profile_url, value: null [2025-09-19 10:56:50,295] nf_core.utils [DEBUG ] Config key: params.validate_params, value: true [2025-09-19 10:56:50,296] nf_core.utils [DEBUG ] Config key: process.cpus, value: { 1 * task.attempt } [2025-09-19 10:56:50,296] nf_core.utils [DEBUG ] Config key: process.memory, value: { 6.GB * task.attempt } [2025-09-19 10:56:50,296] nf_core.utils [DEBUG ] Config key: process.time, value: { 4.h * task.attempt } [2025-09-19 10:56:50,297] nf_core.utils [DEBUG ] Config key: process.errorStrategy, value: { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } [2025-09-19 10:56:50,297] nf_core.utils [DEBUG ] Config key: process.maxRetries, value: 1 [2025-09-19 10:56:50,297] nf_core.utils [DEBUG ] Config key: process.maxErrors, value: -1 [2025-09-19 10:56:50,298] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_single'.cpus, value: { 1 } [2025-09-19 10:56:50,298] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_single'.memory, value: { 6.GB * task.attempt } [2025-09-19 10:56:50,299] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_single'.time, value: { 4.h * task.attempt } [2025-09-19 10:56:50,299] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_low'.cpus, value: { 2 * task.attempt } [2025-09-19 10:56:50,299] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_low'.memory, value: { 12.GB * task.attempt } [2025-09-19 10:56:50,300] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_low'.time, value: { 4.h * task.attempt } [2025-09-19 10:56:50,300] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_medium'.cpus, value: { 6 * task.attempt } [2025-09-19 10:56:50,300] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_medium'.memory, value: { 36.GB * task.attempt } [2025-09-19 10:56:50,301] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_medium'.time, value: { 8.h * task.attempt } [2025-09-19 10:56:50,301] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high'.cpus, value: { 12 * task.attempt } [2025-09-19 10:56:50,302] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high'.memory, value: { 72.GB * task.attempt } [2025-09-19 10:56:50,302] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high'.time, value: { 16.h * task.attempt } [2025-09-19 10:56:50,302] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_long'.time, value: { 20.h * task.attempt } [2025-09-19 10:56:50,303] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high_memory'.memory, value: { 200.GB * task.attempt } [2025-09-19 10:56:50,303] nf_core.utils [DEBUG ] Config key: process.'withLabel:error_ignore'.errorStrategy, value: ignore [2025-09-19 10:56:50,303] nf_core.utils [DEBUG ] Config key: process.'withLabel:error_retry'.errorStrategy, value: retry [2025-09-19 10:56:50,304] nf_core.utils [DEBUG ] Config key: process.'withLabel:error_retry'.maxRetries, value: 2 [2025-09-19 10:56:50,304] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_gpu'.ext.use_gpu, value: { workflow.profile.contains('gpu') } [2025-09-19 10:56:50,305] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_gpu'.accelerator, value: { workflow.profile.contains('gpu') ? 1 : null } [2025-09-19 10:56:50,305] nf_core.utils [DEBUG ] Config key: process.shell, value: ['bash', '-C', '-e', '-u', '-o', 'pipefail'] [2025-09-19 10:56:50,305] nf_core.utils [DEBUG ] Config key: process.publishDir, value: [path:{ "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }] [2025-09-19 10:56:50,306] nf_core.utils [DEBUG ] Config key: process.'withName:FASTQC'.ext.args, value: --quiet [2025-09-19 10:56:50,306] nf_core.utils [DEBUG ] Config key: process.'withName:MULTIQC'.ext.args, value: { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } [2025-09-19 10:56:50,307] nf_core.utils [DEBUG ] Config key: process.'withName:MULTIQC'.publishDir, value: [path:{ "${params.outdir}/multiqc" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }] [2025-09-19 10:56:50,307] nf_core.utils [DEBUG ] Config key: apptainer.registry, value: quay.io [2025-09-19 10:56:50,307] nf_core.utils [DEBUG ] Config key: docker.registry, value: quay.io [2025-09-19 10:56:50,308] nf_core.utils [DEBUG ] Config key: podman.registry, value: quay.io [2025-09-19 10:56:50,308] nf_core.utils [DEBUG ] Config key: singularity.registry, value: quay.io [2025-09-19 10:56:50,308] nf_core.utils [DEBUG ] Config key: charliecloud.registry, value: quay.io [2025-09-19 10:56:50,309] nf_core.utils [DEBUG ] Config key: env.PYTHONNOUSERSITE, value: 1 [2025-09-19 10:56:50,309] nf_core.utils [DEBUG ] Config key: env.R_PROFILE_USER, value: /.Rprofile [2025-09-19 10:56:50,309] nf_core.utils [DEBUG ] Config key: env.R_ENVIRON_USER, value: /.Renviron [2025-09-19 10:56:50,310] nf_core.utils [DEBUG ] Config key: env.JULIA_DEPOT_PATH, value: /usr/local/share/julia [2025-09-19 10:56:50,310] nf_core.utils [DEBUG ] Config key: nextflow.enable.configProcessNamesValidation, value: false [2025-09-19 10:56:50,310] nf_core.utils [DEBUG ] Config key: timeline.enabled, value: true [2025-09-19 10:56:50,311] nf_core.utils [DEBUG ] Config key: timeline.file, value: null/pipeline_info/execution_timeline_2025-09-19_10-56-49.html [2025-09-19 10:56:50,311] nf_core.utils [DEBUG ] Config key: report.enabled, value: true [2025-09-19 10:56:50,311] nf_core.utils [DEBUG ] Config key: report.file, value: null/pipeline_info/execution_report_2025-09-19_10-56-49.html [2025-09-19 10:56:50,312] nf_core.utils [DEBUG ] Config key: trace.enabled, value: true [2025-09-19 10:56:50,312] nf_core.utils [DEBUG ] Config key: trace.file, value: null/pipeline_info/execution_trace_2025-09-19_10-56-49.txt [2025-09-19 10:56:50,312] nf_core.utils [DEBUG ] Config key: dag.enabled, value: true [2025-09-19 10:56:50,313] nf_core.utils [DEBUG ] Config key: dag.file, value: null/pipeline_info/pipeline_dag_2025-09-19_10-56-49.html [2025-09-19 10:56:50,313] nf_core.utils [DEBUG ] Config key: manifest.name, value: nf-core/testpipeline [2025-09-19 10:56:50,314] nf_core.utils [DEBUG ] Config key: manifest.contributors, value: [[name:'tester', affiliation:'', email:'', github:'', contribution:[], orcid:'']] [2025-09-19 10:56:50,314] nf_core.utils [DEBUG ] Config key: manifest.homePage, value: https://github.com/nf-core/testpipeline [2025-09-19 10:56:50,315] nf_core.utils [DEBUG ] Config key: manifest.description, value: test [2025-09-19 10:56:50,315] nf_core.utils [DEBUG ] Config key: manifest.mainScript, value: main.nf [2025-09-19 10:56:50,315] nf_core.utils [DEBUG ] Config key: manifest.defaultBranch, value: main [2025-09-19 10:56:50,315] nf_core.utils [DEBUG ] Config key: manifest.nextflowVersion, value: !>=24.10.5 [2025-09-19 10:56:50,316] nf_core.utils [DEBUG ] Config key: manifest.version, value: 1.0.0dev [2025-09-19 10:56:50,316] nf_core.utils [DEBUG ] Config key: manifest.doi, value: empty string [2025-09-19 10:56:50,316] nf_core.utils [DEBUG ] Config key: plugins, value: ['nf-schema@2.4.2'] [2025-09-19 10:56:50,317] nf_core.utils [DEBUG ] Config key: validation.defaultIgnoreParams, value: ['genomes'] [2025-09-19 10:56:50,317] nf_core.utils [DEBUG ] Config key: validation.monochromeLogs, value: false [2025-09-19 10:56:50,317] nf_core.utils [DEBUG ] Config key: validation.help.enabled, value: true [2025-09-19 10:56:50,318] nf_core.utils [DEBUG ] Config key: validation.help.command, value: nextflow run nf-core/testpipeline -profile --input samplesheet.csv --outdir [2025-09-19 10:56:50,318] nf_core.utils [DEBUG ] Config key: validation.help.fullParameter, value: help_full [2025-09-19 10:56:50,319] nf_core.utils [DEBUG ] Config key: validation.help.showHiddenParameter, value: show_hidden [2025-09-19 10:56:50,319] nf_core.utils [DEBUG ] Config key: validation.help.beforeText, value: ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/testpipeline 1.0.0dev ------------------------------------------------------ [2025-09-19 10:56:50,320] nf_core.utils [DEBUG ] Config key: validation.help.afterText, value: * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/testpipeline/blob/main/CITATIONS.md [2025-09-19 10:56:50,321] nf_core.utils [DEBUG ] Config key: validation.summary.beforeText, value: ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/testpipeline 1.0.0dev ------------------------------------------------------ [2025-09-19 10:56:50,322] nf_core.utils [DEBUG ] Config key: validation.summary.afterText, value: * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/testpipeline/blob/main/CITATIONS.md [2025-09-19 10:56:50,323] nf_core.utils [DEBUG ] Saving config cache: /Users/matthias.zepper/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json [2025-09-19 10:56:50,324] nf_core.utils [DEBUG ] Using config file: /Users/matthias.zepper/.config/nfcore/nf-core/modules/.nf-core.yml [2025-09-19 10:56:50,325] nf_core.utils [DEBUG ] Got '.' as path [2025-09-19 10:56:50,326] nf_core.utils [DEBUG ] No config cache found [2025-09-19 10:56:50,326] nf_core.utils [DEBUG ] Running command: nextflow config -flat . [2025-09-19 10:56:51,610] nf_core.utils [DEBUG ] Config key: params.input, value: null [2025-09-19 10:56:51,611] nf_core.utils [DEBUG ] Config key: params.multiqc_config, value: null [2025-09-19 10:56:51,611] nf_core.utils [DEBUG ] Config key: params.multiqc_title, value: null [2025-09-19 10:56:51,612] nf_core.utils [DEBUG ] Config key: params.multiqc_logo, value: null [2025-09-19 10:56:51,612] nf_core.utils [DEBUG ] Config key: params.max_multiqc_email_size, value: 25.MB [2025-09-19 10:56:51,612] nf_core.utils [DEBUG ] Config key: params.multiqc_methods_description, value: null [2025-09-19 10:56:51,613] nf_core.utils [DEBUG ] Config key: params.outdir, value: null [2025-09-19 10:56:51,613] nf_core.utils [DEBUG ] Config key: params.publish_dir_mode, value: copy [2025-09-19 10:56:51,613] nf_core.utils [DEBUG ] Config key: params.email, value: null [2025-09-19 10:56:51,614] nf_core.utils [DEBUG ] Config key: params.email_on_fail, value: null [2025-09-19 10:56:51,614] nf_core.utils [DEBUG ] Config key: params.plaintext_email, value: false [2025-09-19 10:56:51,614] nf_core.utils [DEBUG ] Config key: params.monochrome_logs, value: false [2025-09-19 10:56:51,615] nf_core.utils [DEBUG ] Config key: params.hook_url, value: null [2025-09-19 10:56:51,615] nf_core.utils [DEBUG ] Config key: params.help, value: false [2025-09-19 10:56:51,615] nf_core.utils [DEBUG ] Config key: params.help_full, value: false [2025-09-19 10:56:51,616] nf_core.utils [DEBUG ] Config key: params.show_hidden, value: false [2025-09-19 10:56:51,616] nf_core.utils [DEBUG ] Config key: params.version, value: false [2025-09-19 10:56:51,616] nf_core.utils [DEBUG ] Config key: params.pipelines_testdata_base_path, value: https://raw.githubusercontent.com/nf-core/test-datasets/ [2025-09-19 10:56:51,617] nf_core.utils [DEBUG ] Config key: params.trace_report_suffix, value: 2025-09-19_10-56-51 [2025-09-19 10:56:51,617] nf_core.utils [DEBUG ] Config key: params.config_profile_name, value: null [2025-09-19 10:56:51,618] nf_core.utils [DEBUG ] Config key: params.config_profile_description, value: null [2025-09-19 10:56:51,618] nf_core.utils [DEBUG ] Config key: params.custom_config_version, value: master [2025-09-19 10:56:51,619] nf_core.utils [DEBUG ] Config key: params.custom_config_base, value: https://raw.githubusercontent.com/nf-core/configs/master [2025-09-19 10:56:51,619] nf_core.utils [DEBUG ] Config key: params.config_profile_contact, value: null [2025-09-19 10:56:51,619] nf_core.utils [DEBUG ] Config key: params.config_profile_url, value: null [2025-09-19 10:56:51,620] nf_core.utils [DEBUG ] Config key: params.validate_params, value: true [2025-09-19 10:56:51,620] nf_core.utils [DEBUG ] Config key: process.cpus, value: { 1 * task.attempt } [2025-09-19 10:56:51,620] nf_core.utils [DEBUG ] Config key: process.memory, value: { 6.GB * task.attempt } [2025-09-19 10:56:51,621] nf_core.utils [DEBUG ] Config key: process.time, value: { 4.h * task.attempt } [2025-09-19 10:56:51,621] nf_core.utils [DEBUG ] Config key: process.errorStrategy, value: { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } [2025-09-19 10:56:51,622] nf_core.utils [DEBUG ] Config key: process.maxRetries, value: 1 [2025-09-19 10:56:51,622] nf_core.utils [DEBUG ] Config key: process.maxErrors, value: -1 [2025-09-19 10:56:51,622] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_single'.cpus, value: { 1 } [2025-09-19 10:56:51,623] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_single'.memory, value: { 6.GB * task.attempt } [2025-09-19 10:56:51,623] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_single'.time, value: { 4.h * task.attempt } [2025-09-19 10:56:51,624] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_low'.cpus, value: { 2 * task.attempt } [2025-09-19 10:56:51,624] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_low'.memory, value: { 12.GB * task.attempt } [2025-09-19 10:56:51,624] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_low'.time, value: { 4.h * task.attempt } [2025-09-19 10:56:51,625] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_medium'.cpus, value: { 6 * task.attempt } [2025-09-19 10:56:51,625] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_medium'.memory, value: { 36.GB * task.attempt } [2025-09-19 10:56:51,625] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_medium'.time, value: { 8.h * task.attempt } [2025-09-19 10:56:51,626] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high'.cpus, value: { 12 * task.attempt } [2025-09-19 10:56:51,626] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high'.memory, value: { 72.GB * task.attempt } [2025-09-19 10:56:51,626] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high'.time, value: { 16.h * task.attempt } [2025-09-19 10:56:51,627] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_long'.time, value: { 20.h * task.attempt } [2025-09-19 10:56:51,627] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_high_memory'.memory, value: { 200.GB * task.attempt } [2025-09-19 10:56:51,628] nf_core.utils [DEBUG ] Config key: process.'withLabel:error_ignore'.errorStrategy, value: ignore [2025-09-19 10:56:51,628] nf_core.utils [DEBUG ] Config key: process.'withLabel:error_retry'.errorStrategy, value: retry [2025-09-19 10:56:51,628] nf_core.utils [DEBUG ] Config key: process.'withLabel:error_retry'.maxRetries, value: 2 [2025-09-19 10:56:51,629] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_gpu'.ext.use_gpu, value: { workflow.profile.contains('gpu') } [2025-09-19 10:56:51,629] nf_core.utils [DEBUG ] Config key: process.'withLabel:process_gpu'.accelerator, value: { workflow.profile.contains('gpu') ? 1 : null } [2025-09-19 10:56:51,630] nf_core.utils [DEBUG ] Config key: process.shell, value: ['bash', '-C', '-e', '-u', '-o', 'pipefail'] [2025-09-19 10:56:51,630] nf_core.utils [DEBUG ] Config key: process.publishDir, value: [path:{ "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }] [2025-09-19 10:56:51,631] nf_core.utils [DEBUG ] Config key: process.'withName:FASTQC'.ext.args, value: --quiet [2025-09-19 10:56:51,631] nf_core.utils [DEBUG ] Config key: process.'withName:MULTIQC'.ext.args, value: { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } [2025-09-19 10:56:51,632] nf_core.utils [DEBUG ] Config key: process.'withName:MULTIQC'.publishDir, value: [path:{ "${params.outdir}/multiqc" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }] [2025-09-19 10:56:51,632] nf_core.utils [DEBUG ] Config key: apptainer.registry, value: quay.io [2025-09-19 10:56:51,632] nf_core.utils [DEBUG ] Config key: docker.registry, value: quay.io [2025-09-19 10:56:51,633] nf_core.utils [DEBUG ] Config key: podman.registry, value: quay.io [2025-09-19 10:56:51,633] nf_core.utils [DEBUG ] Config key: singularity.registry, value: quay.io [2025-09-19 10:56:51,633] nf_core.utils [DEBUG ] Config key: charliecloud.registry, value: quay.io [2025-09-19 10:56:51,634] nf_core.utils [DEBUG ] Config key: env.PYTHONNOUSERSITE, value: 1 [2025-09-19 10:56:51,634] nf_core.utils [DEBUG ] Config key: env.R_PROFILE_USER, value: /.Rprofile [2025-09-19 10:56:51,634] nf_core.utils [DEBUG ] Config key: env.R_ENVIRON_USER, value: /.Renviron [2025-09-19 10:56:51,635] nf_core.utils [DEBUG ] Config key: env.JULIA_DEPOT_PATH, value: /usr/local/share/julia [2025-09-19 10:56:51,635] nf_core.utils [DEBUG ] Config key: nextflow.enable.configProcessNamesValidation, value: false [2025-09-19 10:56:51,635] nf_core.utils [DEBUG ] Config key: timeline.enabled, value: true [2025-09-19 10:56:51,636] nf_core.utils [DEBUG ] Config key: timeline.file, value: null/pipeline_info/execution_timeline_2025-09-19_10-56-51.html [2025-09-19 10:56:51,636] nf_core.utils [DEBUG ] Config key: report.enabled, value: true [2025-09-19 10:56:51,636] nf_core.utils [DEBUG ] Config key: report.file, value: null/pipeline_info/execution_report_2025-09-19_10-56-51.html [2025-09-19 10:56:51,637] nf_core.utils [DEBUG ] Config key: trace.enabled, value: true [2025-09-19 10:56:51,637] nf_core.utils [DEBUG ] Config key: trace.file, value: null/pipeline_info/execution_trace_2025-09-19_10-56-51.txt [2025-09-19 10:56:51,637] nf_core.utils [DEBUG ] Config key: dag.enabled, value: true [2025-09-19 10:56:51,638] nf_core.utils [DEBUG ] Config key: dag.file, value: null/pipeline_info/pipeline_dag_2025-09-19_10-56-51.html [2025-09-19 10:56:51,638] nf_core.utils [DEBUG ] Config key: manifest.name, value: nf-core/testpipeline [2025-09-19 10:56:51,639] nf_core.utils [DEBUG ] Config key: manifest.contributors, value: [[name:'tester', affiliation:'', email:'', github:'', contribution:[], orcid:'']] [2025-09-19 10:56:51,639] nf_core.utils [DEBUG ] Config key: manifest.homePage, value: https://github.com/nf-core/testpipeline [2025-09-19 10:56:51,639] nf_core.utils [DEBUG ] Config key: manifest.description, value: test [2025-09-19 10:56:51,640] nf_core.utils [DEBUG ] Config key: manifest.mainScript, value: main.nf [2025-09-19 10:56:51,640] nf_core.utils [DEBUG ] Config key: manifest.defaultBranch, value: main [2025-09-19 10:56:51,640] nf_core.utils [DEBUG ] Config key: manifest.nextflowVersion, value: !>=24.10.5 [2025-09-19 10:56:51,641] nf_core.utils [DEBUG ] Config key: manifest.version, value: 1.0.0dev [2025-09-19 10:56:51,641] nf_core.utils [DEBUG ] Config key: manifest.doi, value: empty string [2025-09-19 10:56:51,641] nf_core.utils [DEBUG ] Config key: plugins, value: ['nf-schema@2.4.2'] [2025-09-19 10:56:51,642] nf_core.utils [DEBUG ] Config key: validation.defaultIgnoreParams, value: ['genomes'] [2025-09-19 10:56:51,642] nf_core.utils [DEBUG ] Config key: validation.monochromeLogs, value: false [2025-09-19 10:56:51,642] nf_core.utils [DEBUG ] Config key: validation.help.enabled, value: true [2025-09-19 10:56:51,643] nf_core.utils [DEBUG ] Config key: validation.help.command, value: nextflow run nf-core/testpipeline -profile --input samplesheet.csv --outdir [2025-09-19 10:56:51,643] nf_core.utils [DEBUG ] Config key: validation.help.fullParameter, value: help_full [2025-09-19 10:56:51,643] nf_core.utils [DEBUG ] Config key: validation.help.showHiddenParameter, value: show_hidden [2025-09-19 10:56:51,644] nf_core.utils [DEBUG ] Config key: validation.help.beforeText, value: ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/testpipeline 1.0.0dev ------------------------------------------------------ [2025-09-19 10:56:51,645] nf_core.utils [DEBUG ] Config key: validation.help.afterText, value: * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/testpipeline/blob/main/CITATIONS.md [2025-09-19 10:56:51,646] nf_core.utils [DEBUG ] Config key: validation.summary.beforeText, value: ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/testpipeline 1.0.0dev ------------------------------------------------------ [2025-09-19 10:56:51,647] nf_core.utils [DEBUG ] Config key: validation.summary.afterText, value: * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/testpipeline/blob/main/CITATIONS.md [2025-09-19 10:56:51,648] nf_core.utils [DEBUG ] Saving config cache: /Users/matthias.zepper/.nextflow/nf-core/wf-config-cache-c793aa7bbd1c9ecc154688e60.json [2025-09-19 10:56:51,649] nf_core.utils [DEBUG ] Using config file: .nf-core.yml [2025-09-19 10:56:51,649] git.util [DEBUG ] sys.platform='darwin', git_executable='git' [2025-09-19 10:56:51,650] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/Users/matthias.zepper/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-09-19 10:56:51,921] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/Users/matthias.zepper/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-09-19 10:56:51,936] nf_core.utils [DEBUG ] Got '/Users/matthias.zepper/.config/nfcore/nf-core/modules' as path [2025-09-19 10:56:51,937] nf_core.utils [DEBUG ] Found a config cache, loading: /Users/matthias.zepper/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json [2025-09-19 10:56:51,937] nf_core.utils [DEBUG ] Using config file: /Users/matthias.zepper/.config/nfcore/nf-core/modules/.nf-core.yml [2025-09-19 10:56:51,956] nf_core.commands_modules [ERROR ] 'decoupler'