Dev2rc #107

jianhong · 2024-04-03T21:47:30Z

PR checklist

…_KTIMPORTTEXT

…code from github.

…nto dev2rc

… into dev2rc

…2rc.

github-actions · 2024-04-03T21:50:21Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit e070217

+| ✅ 384 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-hicar_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-hicar_logo_light.png
files_exist - File found: docs/images/nf-core-hicar_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-hicar_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowHicar.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 2.0.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.method= HiCAR
nextflow_config - Config default value correct: params.enzyme= CviQI
nextflow_config - Config default value correct: params.restriction_sites= ^TAC
nextflow_config - Config default value correct: params.restriction_sites_cut_off= 0.5
nextflow_config - Config default value correct: params.cutadapt_5end= ^TAC
nextflow_config - Config default value correct: params.cutadapt_3end= skip
nextflow_config - Config default value correct: params.cutadapt_minimum_length= 50:50
nextflow_config - Config default value correct: params.cutadapt_action= trim
nextflow_config - Config default value correct: params.cutadapt_error_tolerance= 0.15
nextflow_config - Config default value correct: params.pairtools_parse_params= --min-mapq 10 --max-molecule-size 2000 --max-inter-align-gap 50 --walks-policy mask --no-flip --drop-seq --drop-sam
nextflow_config - Config default value correct: params.pairtools_parse2_params= --min-mapq 10 --max-insert-size 2000 --max-inter-align-gap 50 --report-position outer --add-pair-index --no-flip --drop-seq --expand --max-expansion-depth 6
nextflow_config - Config default value correct: params.pairtools_parse_version= parse
nextflow_config - Config default value correct: params.shiftsize= -75
nextflow_config - Config default value correct: params.smooth_window= 150
nextflow_config - Config default value correct: params.qval_thresh= 0.01
nextflow_config - Config default value correct: params.cool_bin= 5000_10000
nextflow_config - Config default value correct: params.maps_cutoff_counts= 12
nextflow_config - Config default value correct: params.maps_cutoff_fold_change= 2.0
nextflow_config - Config default value correct: params.maps_cutoff_fdr= 2.0
nextflow_config - Config default value correct: params.maps_filter= None
nextflow_config - Config default value correct: params.maps_model= pospoisson
nextflow_config - Config default value correct: params.snow_type= SOCK
nextflow_config - Config default value correct: params.peak_pair_block= 100000000.0
nextflow_config - Config default value correct: params.min_counts_per_loop= 1
nextflow_config - Config default value correct: params.hicdcplus_cutoff_fdr= 0.05
nextflow_config - Config default value correct: params.peakachu_pretrained_url= http://3dgenome.fsm.northwestern.edu/peakachu/HiCAR-models/HiCAR-peakachu-pretrained.
nextflow_config - Config default value correct: params.r1_pval_thresh= 0.1
nextflow_config - Config default value correct: params.res_compartments= 100000
nextflow_config - Config default value correct: params.res_tads= 10000
nextflow_config - Config default value correct: params.tad_tool= hicexplorer
nextflow_config - Config default value correct: params.apa_tool= hicexplorer
nextflow_config - Config default value correct: params.apa_format= pdf
nextflow_config - Config default value correct: params.compartments_tool= cooltools
nextflow_config - Config default value correct: params.interactions_tool= maps
nextflow_config - Config default value correct: params.da_tool= diffhic
nextflow_config - Config default value correct: params.v4c_tool= hicexplorer
nextflow_config - Config default value correct: params.tfea_tool= homer
nextflow_config - Config default value correct: params.juicer_tools_jar= https://github.com/aidenlab/JuicerTools/releases/download/v3.0.0/juicer_tools.3.0.0.jar
nextflow_config - Config default value correct: params.juicer_norm_method= SCALE
nextflow_config - Config default value correct: params.peak_interactions_threshold= 2
nextflow_config - Config default value correct: params.maps_3d_ext= sig3Dinteractions.pe.txt
nextflow_config - Config default value correct: params.long_bedpe_postfix= long.bedpe
nextflow_config - Config default value correct: params.short_bed_postfix= shrt.vip.bed
nextflow_config - Config default value correct: params.v4c_max_events= 25
nextflow_config - Config default value correct: params.hic_tools_jar= https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 240.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nextflow_config - Config default value correct: params.kraken2_db= https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20230605.tar.gz
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-hicar_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hicar_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hicar_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (357 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - CHECKSUMS found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BIGWIGAVERAGEOVERBED found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBL_UCSC_CONVERT found in conf/modules.config and Nextflow scripts.
modules_config - BEDGRAPH_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - WIG_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - GET_SCALE found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_DIGEST found in conf/modules.config and Nextflow scripts.
modules_config - RE_CUTSITE found in conf/modules.config and Nextflow scripts.
modules_config - GENOME_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - CHROMSIZES found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - GENMAP_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - GENMAP_MAPPABILITY found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_WIGTOBIGWIG found in conf/modules.config and Nextflow scripts.
modules_config - GTF2BED found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_GTF found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_GFF found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_GENE_BED found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_ADDITIONAL_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_SUBSETLOOPS found in conf/modules.config and Nextflow scripts.
modules_config - BEDPE2BED found in conf/modules.config and Nextflow scripts.
modules_config - CUTADAPT_5END found in conf/modules.config and Nextflow scripts.
modules_config - CUTADAPT_3END found in conf/modules.config and Nextflow scripts.
modules_config - CAT_CUTADAPT_R1 found in conf/modules.config and Nextflow scripts.
modules_config - CAT_CUTADAPT_R2 found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_IDXSTATS found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_PARSE found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_PARSE2 found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_FLIP found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_SELECT_VP found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_DEDUP found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_RESTRICT found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_SELECT_LONG found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_PAIRS2HDF5 found in conf/modules.config and Nextflow scripts.
modules_config - PAIRIX found in conf/modules.config and Nextflow scripts.
modules_config - READS_STAT found in conf/modules.config and Nextflow scripts.
modules_config - READS_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - PAIRSQC found in conf/modules.config and Nextflow scripts.
modules_config - PAIRSPLOT found in conf/modules.config and Nextflow scripts.
modules_config - DUMP4HOMER found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_LOAD found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_CLOAD found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_BALANCE found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_ZOOMIFY found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_DUMP_PER_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_DUMP_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - DUMPREADS_PER_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - DUMPREADS_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - JUICER_PRE found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_SELECT_SHORT found in conf/modules.config and Nextflow scripts.
modules_config - SHIFT_READS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_READS found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_GENOMECOV_PER_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - MACS2_CALLPEAK found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_PEAK found in conf/modules.config and Nextflow scripts.
modules_config - ATACQC found in conf/modules.config and Nextflow scripts.
modules_config - DUMP_READS_PER_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - BEDFILES_SORT_PER_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDCLIP found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG_PER_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - DUMP_READS_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_GENOMECOV_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - BEDFILES_SORT_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_INTERACTIONS found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_ENZYMECUT found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_CUT found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_FEND found in conf/modules.config and Nextflow scripts.
modules_config - SEQLEVELS_STYLE found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBL_UCSC_CONVERT1 found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBL_UCSC_CONVERT2 found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_FEATURE found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_MAPS found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_CALLPEAK found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_REFORMAT found in conf/modules.config and Nextflow scripts.
modules_config - MAPS_RAW2BG2 found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_ZOOMIFY_MAPS found in conf/modules.config and Nextflow scripts.
modules_config - HICDCPLUS_FEATURES found in conf/modules.config and Nextflow scripts.
modules_config - HICDCPLUS_CALL_LOOPS found in conf/modules.config and Nextflow scripts.
modules_config - PEAKACHU_MODEL found in conf/modules.config and Nextflow scripts.
modules_config - PEAKACHU_SCORE found in conf/modules.config and Nextflow scripts.
modules_config - CAT_HOMER found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_MAKETAGDIRECTORY found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_FINDTADSANDLOOPS found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_FINDTADSANDLOOPS_TADS found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_INSTALL found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_RUNHICPCA found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_FINDHICCOMPARTMENTS found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG_HOMER_COMPARTMENTS found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_FINDMOTIFSGENOME found in conf/modules.config and Nextflow scripts.
modules_config - COOLTOOLS_EIGSCIS found in conf/modules.config and Nextflow scripts.
modules_config - COOLTOOLS_INSULATION found in conf/modules.config and Nextflow scripts.
modules_config - COOLTOOLS_PILEUP found in conf/modules.config and Nextflow scripts.
modules_config - PLOTNPZ_BY_COOLTOOLS found in conf/modules.config and Nextflow scripts.
modules_config - VIRTUAL4C_BY_COOLTOOLS found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICCORRECTMATRIX found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICPCA found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICTRANSFORM found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICPLOTMATRIX_PCA1 found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICPLOTMATRIX_PCA2 found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICFINDTADS found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICPLOTTADS found in conf/modules.config and Nextflow scripts.
modules_config - RECENTER_PEAK found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_CHICQUALITYCONTROL found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_CHICVIEWPOINTBACKGROUNDMODEL found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_CHICVIEWPOINT found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_CHICSIGNIFICANTINTERACTIONS found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_CHICAGGREGATESTATISTIC found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_CHICDIFFERENTIALTEST found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_CHICPLOTVIEWPOINT found in conf/modules.config and Nextflow scripts.
modules_config - HICEXPLORER_HICAGGREGATECONTACTS found in conf/modules.config and Nextflow scripts.
modules_config - JUICER_ADDNORM found in conf/modules.config and Nextflow scripts.
modules_config - JUICER_EIGENVECTOR found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG_JUICER_EIGENVECTOR found in conf/modules.config and Nextflow scripts.
modules_config - JUICER_APA found in conf/modules.config and Nextflow scripts.
modules_config - R1READS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_R1READS found in conf/modules.config and Nextflow scripts.
modules_config - CALL_R1PEAK found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_R1PEAK found in conf/modules.config and Nextflow scripts.
modules_config - DUMP_R1_READS_PER_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG_PER_R1_GROUP found in conf/modules.config and Nextflow scripts.
modules_config - DUMP_R1_READS_PER_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_GENOMECOV_PER_R1_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_BEDGRAPHTOBIGWIG_PER_R1_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - BEDPE2BED_HI found in conf/modules.config and Nextflow scripts.
modules_config - BEDPE2BED_DIFF found in conf/modules.config and Nextflow scripts.
modules_config - PREPARE_COUNTS found in conf/modules.config and Nextflow scripts.
modules_config - POST_COUNTS found in conf/modules.config and Nextflow scripts.
modules_config - CALL_HIPEAK found in conf/modules.config and Nextflow scripts.
modules_config - ASSIGN_TYPE found in conf/modules.config and Nextflow scripts.
modules_config - ADJUST_COMPARTMENTS found in conf/modules.config and Nextflow scripts.
modules_config - DIFFERENTIAL_COMPARTMENTS found in conf/modules.config and Nextflow scripts.
modules_config - DIFFHICAR found in conf/modules.config and Nextflow scripts.
modules_config - DIFFHIC found in conf/modules.config and Nextflow scripts.
modules_config - DIFFSET found in conf/modules.config and Nextflow scripts.
modules_config - DIFF_HIPEAK found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_CHIPPEAKANNO found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_CHIPPEAKANNO_HIPEAK found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_CHIPPEAKANNO_DIFFHIPEAK found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_ENRICH found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_ATACSEQTFEA found in conf/modules.config and Nextflow scripts.
modules_config - BIOC_TRACKVIEWER found in conf/modules.config and Nextflow scripts.
modules_config - IGV found in conf/modules.config and Nextflow scripts.
modules_config - CIRCOS_PREPARE found in conf/modules.config and Nextflow scripts.
modules_config - CIRCOS found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_COMBINEKREPORTS found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_KREPORT2KRONA found in conf/modules.config and Nextflow scripts.
modules_config - KRONA_KTIMPORTTEXT found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-07-12 20:26:00

… into dev2rc

jianhong and others added 30 commits July 19, 2023 15:03

export more cutadapt parameters.

7ca9f17

export more cutadapt parameters.

3dd9f7c

push the changes for last submit.

337e755

add function to detect the contamination by karken2.

a349011

export pairtools_walks_policy parameter.

cac169c

update changelog.

10be2f7

update the pipeline to skip cutadapt_3end by default.

5f966bd

fix the wrong input for cutadapt_3end.

5e6febe

update the keywords to skip cutadapt 3end.

6f15719

use the standard kraken2 db as default.

a47d456

change the cutadapt_action default setting.

190554f

Merge branch 'dev' into dev2rc; fix the file name collision for KRONA…

72baac1

…_KTIMPORTTEXT

run black to fix the python script format.

b8a2f29

change the version number to 2.0.0dev.

6653593

update to nf-core/samtools/sort

95664b9

fix a typo in nextflow_schema.json.

bd24b34

try to fix the multiqc_config.yml missing report_comment error.

4834e52

try again.

491348f

update igv.js tracks to avoid the error that if skip interaction caller.

097bdf3

fix a bug in creating maps signal cooler file.

79e59df

export the filtered pairs files.

18c7c68

add control for skip circos.

cb7ed09

fix a bug that if genome fastq file can not be handled by the bwa index.

a8f5d91

update the Channel of genome fasta.

199e586

add output controler for pairs file.

fbb14db

Template update for nf-core/tools version 2.10

a3040ce

add parse2 module.

6445db7

fix the sort memory issue (exit code 139 with fragment fault)

a52e1c8

add tmpdir parameter for pairtools sort.

6f92af8

try to fix the pairtools sort memory issue.

7bb8856

jianhong and others added 17 commits October 10, 2023 17:40

add same fragement stats and change the TSSEscre calculation range.

ca243ea

fix the potential issue if the container can not download the source …

9fbf57d

…code from github.

update pairtools/sort

c4eb5e2

Merge remote-tracking branch 'upstream/nf-core-template-merge-2.10' i…

65e6370

…nto dev2rc

fix the space issue.

1672d78

update the citation in WorkflowHicar.groovy

92f03cf

remove dev from multiqc_config.yml

53811a6

Template update for nf-core/tools version 2.11

8f706e5

Template update for nf-core/tools version 2.11.1

e5dcc4b

Template update for nf-core/tools version 2.12

03f093d

Template update for nf-core/tools version 2.13

207b0d9

Merge remote-tracking branch 'upstream/nf-core-template-merge-2.11.1'…

0b2e8db

… into dev2rc

update the pairtools to newest module.

a2f608e

Template update for nf-core/tools version 2.13.1

fab2116

add adjust and de A/B compartments.

bc8de9e

Merge remote-tracking branch 'upstream/nf-core-merge-2.13.1' into dev…

5a34230

…2rc.

update the CHANGELOG.md

863eed1

jianhong and others added 11 commits April 4, 2024 08:32

fix the lint.

69b3bc5

update the dark logo.

9c220b0

try to fix the null fasta issue.

3ea4292

fix the compartment caller for hicexplorer.

814dc09

Template update for nf-core/tools version 2.14.0

fc199b6

Template update for nf-core/tools version 2.14.1

23861e4

Merge remote-tracking branch 'upstream/nf-core-template-merge-2.14.1'…

95a66e0

… into dev2rc

update output of differential_compartments.nf

d5460d1

trun on publish the filtered valid pairs.

5a45bb6

fix the version output issue with warning export.

e901ebe

temp fix the version output issue for genmap.

e070217

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jianhong commented Apr 3, 2024

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nf-core lint overall result: Passed ✅ ⚠️

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`nf-core lint` overall result: Passed ✅ ⚠️