From 9ff5a1ee2feb10a875c02db29bfa7b4f49a3d5aa Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 14 Jul 2023 11:59:04 +0200 Subject: [PATCH 01/15] Adding new qualimap --- CITATIONS.md | 4 + conf/modules.config | 8 ++ docs/output.md | 27 ++++++ modules.json | 5 + modules/nf-core/qualimap/bamqc/main.nf | 123 ++++++++++++++++++++++++ modules/nf-core/qualimap/bamqc/meta.yml | 47 +++++++++ nextflow.config | 4 + nextflow_schema.json | 8 ++ workflows/eager.nf | 21 ++++ 9 files changed, 247 insertions(+) create mode 100644 modules/nf-core/qualimap/bamqc/main.nf create mode 100644 modules/nf-core/qualimap/bamqc/meta.yml diff --git a/CITATIONS.md b/CITATIONS.md index 11f540b91..5f6a4c981 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -62,6 +62,10 @@ > Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature Methods, 10(4), 325–327. doi: [10.1038/nmeth.2375](https://doi.org/10.1038/nmeth.2375) +- [QualiMap](https://doi.org/10.1093/bioinformatics/btv566) + + > QualiMap Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics , 32(2), 292–294. Download: http://qualimap.bioinfo.cipf.es/ + - [DamageProfiler](https://doi.org/10.1093/bioinformatics/btab190) > DamageProfiler Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. In Bioinformatics (btab190). doi: [10.1093/bioinformatics/btab190](https://doi.org/10.1093/bioinformatics/btab190). Download: https://github.com/Integrative-Transcriptomics/DamageProfiler diff --git a/conf/modules.config b/conf/modules.config index f8131987b..57da3be20 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -499,6 +499,14 @@ process { ] } + withName: "QUALIMAP_BAMQC" { + publishDir = [ + path: { "${params.outdir}/mapstats/qualimap" }, + mode: params.publish_dir_mode, + enabled: true + ] + } + withName: "DAMAGEPROFILER" { ext.args = [ "-l ${params.damageprofiler_length}", diff --git a/docs/output.md b/docs/output.md index 13520a4c4..950715db7 100644 --- a/docs/output.md +++ b/docs/output.md @@ -266,6 +266,33 @@ The resulting histogram file will contain estimated deduplication statistics at These curves will be displayed in the pipeline run's MultiQC report, however you can also use this file for plotting yourself for further exploration e.g. in R to find your sequencing target depth. +#### QualiMap + +
+Output files + +- `qualimap/` + + - `/` + - `*.html`: in-depth report including percent coverage, depth coverage, GC content, etc. of mapped reads + - `genome_results.txt` + - `css/`: HTML CSS styling used for the report + - `images_qualimapReport/`: PNG version of images from the HTML report. + - `raw_data_qualimapReport/`: The raw data used to render the HTML report as TXT files. + +
+ +[QualiMap](http://qualimap.bioinfo.cipf.es/) +is a tool which provides statistics on the quality of the mapping of your reads to your reference genome. It allows you to assess how well covered your reference genome is by your data, both in 'fold' depth (average number of times a given base on the reference is covered by a read) and 'percentage' (the percentage of all bases on the reference genome that is covered at a given fold depth). These outputs allow you to make decision if you have enough quality data for downstream applications like genotyping, and how to adjust the parameters for those tools accordingly. + +> NB: Neither fold coverage nor percent coverage on there own is sufficient to assess whether you have a high quality mapping. Abnormally high fold coverages of a smaller region such as highly conserved genes or un-removed-adapter-containing reference genomes can artificially inflate the mean coverage, yet a high percent coverage is not useful if all bases of the genome are covered at just 1x coverage. + +**Note that many of the statistics from this module are displayed in the General Stats table, as they represent single values that are not plottable.** + +You will receive output for each sample. This means you will statistics of deduplicated values of all types of libraries combined in a single value (i.e. non-UDG treated, full-UDG, paired-end, single-end all together). + +> ⚠️ Warning: If your library has no reads mapping to the reference, this will result in an empty BAM file. Qualimap will therefore not produce any output even if a BAM exists! + #### DamageProfiler
diff --git a/modules.json b/modules.json index e96f3ee4f..a566f1cd2 100644 --- a/modules.json +++ b/modules.json @@ -125,6 +125,11 @@ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, + "qualimap/bamqc": { + "branch": "master", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] + }, "samtools/faidx": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf new file mode 100644 index 000000000..fef7307a0 --- /dev/null +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -0,0 +1,123 @@ +process QUALIMAP_BAMQC { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::qualimap=2.2.2d" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : + 'biocontainers/qualimap:2.2.2d--1' }" + + input: + tuple val(meta), path(bam) + path gff + + output: + tuple val(meta), path("${prefix}"), emit: results + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' + def memory = (task.memory.mega*0.8).intValue() + 'M' + def regions = gff ? "--gff $gff" : '' + + def strandedness = 'non-strand-specific' + if (meta.strandedness == 'forward') { + strandedness = 'strand-specific-forward' + } else if (meta.strandedness == 'reverse') { + strandedness = 'strand-specific-reverse' + } + """ + unset DISPLAY + mkdir -p tmp + export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp + qualimap \\ + --java-mem-size=$memory \\ + bamqc \\ + $args \\ + -bam $bam \\ + $regions \\ + -p $strandedness \\ + $collect_pairs \\ + -outdir $prefix \\ + -nt $task.cpus + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') + END_VERSIONS + """ + + stub: + prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + """ + mkdir -p $prefix/css + mkdir $prefix/images_qualimapReport + mkdir $prefix/raw_data_qualimapReport + cd $prefix/css + touch agogo.css + touch basic.css + touch bgtop.png + touch comment-close.png + touch doctools.js + touch down-pressed.png + touch jquery.js + touch plus.png + touch qualimap_logo_small.png + touch searchtools.js + touch up.png + touch websupport.js + touch ajax-loader.gif + touch bgfooter.png + touch comment-bright.png + touch comment.png + touch down.png + touch file.png + touch minus.png + touch pygments.css + touch report.css + touch underscore.js + touch up-pressed.png + cd ../images_qualimapReport/ + touch genome_coverage_0to50_histogram.png + touch genome_coverage_quotes.png + touch genome_insert_size_across_reference.png + touch genome_mapping_quality_histogram.png + touch genome_uniq_read_starts_histogram.png + touch genome_coverage_across_reference.png + touch genome_gc_content_per_window.png + touch genome_insert_size_histogram.png + touch genome_reads_clipping_profile.png + touch genome_coverage_histogram.png + touch genome_homopolymer_indels.png + touch genome_mapping_quality_across_reference.png + touch genome_reads_content_per_read_position.png + cd ../raw_data_qualimapReport + touch coverage_across_reference.txt + touch genome_fraction_coverage.txt + touch insert_size_histogram.txt + touch mapped_reads_nucleotide_content.txt + touch coverage_histogram.txt + touch homopolymer_indels.txt + touch mapped_reads_clipping_profile.txt + touch mapping_quality_across_reference.txt + touch duplication_rate_histogram.txt + touch insert_size_across_reference.txt + touch mapped_reads_gc-content_distribution.txt + touch mapping_quality_histogram.txt + cd ../ + touch genome_results.txt + touch qualimapReport.html + cd ../ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml new file mode 100644 index 000000000..303532eb7 --- /dev/null +++ b/modules/nf-core/qualimap/bamqc/meta.yml @@ -0,0 +1,47 @@ +name: qualimap_bamqc +description: Evaluate alignment data +keywords: + - quality control + - qc + - bam +tools: + - qualimap: + description: | + Qualimap 2 is a platform-independent application written in + Java and R that provides both a Graphical User Interface and + a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts. + homepage: http://qualimap.bioinfo.cipf.es/ + documentation: http://qualimap.conesalab.org/doc_html/index.html + doi: 10.1093/bioinformatics/bts503 + licence: ["GPL-2.0-only"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results: + type: dir + description: Qualimap results dir + pattern: "*/*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@phue" diff --git a/nextflow.config b/nextflow.config index e918e9d8a..d6ddfb611 100644 --- a/nextflow.config +++ b/nextflow.config @@ -129,6 +129,10 @@ params { skip_deduplication = false deduplication_tool = 'markduplicates' + // Qualimap + skip_qualimap = false + snpcapture_bed = null + // MtNucRatio run_mtnucratio = false mitochondrion_header = 'MT' diff --git a/nextflow_schema.json b/nextflow_schema.json index 19838b4e7..b28033c22 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -789,6 +789,14 @@ "description": "Turns on defects mode to extrapolate without testing for defects (lc_extrap mode only).", "help_text": "Activates defects mode of `lc_extrap`, which does the extrapolation without testing for defects.\n\n> Modifies preseq lc_extrap parameter: `-D`", "fa_icon": "fab fa-creative-commons-sampling-plus" + }, + "skip_qualimap": { + "type": "boolean", + "default": "false" + }, + "snpcapture_bed": { + "type": "string", + "description": "Path to snp capture BED" } }, "fa_icon": "fas fa-search" diff --git a/workflows/eager.nf b/workflows/eager.nf index 08d1f19fb..af99e92a6 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -86,6 +86,7 @@ include { PRESEQ_CCURVE } from '../modules/nf-core/preseq/ccurve/m include { PRESEQ_LCEXTRAP } from '../modules/nf-core/preseq/lcextrap/main' include { FALCO } from '../modules/nf-core/falco/main' include { MTNUCRATIO } from '../modules/nf-core/mtnucratio/main' +include { QUALIMAP_BAMQC } from '../modules/nf-core/qualimap/bamqc/main' /* @@ -123,6 +124,13 @@ workflow EAGER { if ( params.preprocessing_tool == 'fastp' && !adapterlist.extension.matches(".*(fa|fasta|fna|fas)") ) error "[nf-core/eager] ERROR: fastp adapter list requires a `.fasta` format and extension (or fa, fas, fna). Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}" } + // QualiMap + if ( params.snpcapture_bed ) { + ch_snpcapture_bed = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect() + } else { + ch_snpcapture_bed = [] + } + // // SUBWORKFLOW: Read in samplesheet, validate and stage input files // @@ -233,6 +241,19 @@ workflow EAGER { ch_dedupped_flagstat = Channel.empty() } + // + // MODULE QUALIMAP + // + + if ( !params.skip_qualimap ) { + ch_qualimap_input = ch_dedupped_bams + .map { + meta, bam, bai -> + [ meta, bam ] + } + QUALIMAP_BAMQC(ch_qualimap_input, ch_snpcapture_bed) + } + // // Section: Metagenomics screening // From 3596bcdc3c2ec0fc879e0d342804d02eb6c93d77 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 21 Jul 2023 12:09:09 +0200 Subject: [PATCH 02/15] Apply suggestions from code review --- docs/output.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index a6531b7c9..33b939987 100644 --- a/docs/output.md +++ b/docs/output.md @@ -406,7 +406,6 @@ You will receive output for each sample. This means you will statistics of dedup > ⚠️ Warning: If your library has no reads mapping to the reference, this will result in an empty BAM file. Qualimap will therefore not produce any output even if a BAM exists! - #### Bedtools
From 169726b376a819110a09abdb1eede93f22fe5426 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 21 Jul 2023 12:10:02 +0200 Subject: [PATCH 03/15] Apply suggestions from code review --- workflows/eager.nf | 9 --------- 1 file changed, 9 deletions(-) diff --git a/workflows/eager.nf b/workflows/eager.nf index ed03b42ac..224699916 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -87,15 +87,6 @@ include { CALCULATE_DAMAGE } from '../subworkflows/local/calculate_ // MODULE: Installed directly from nf-core/modules // -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' -include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/main' -include { PRESEQ_CCURVE } from '../modules/nf-core/preseq/ccurve/main' -include { PRESEQ_LCEXTRAP } from '../modules/nf-core/preseq/lcextrap/main' -include { FALCO } from '../modules/nf-core/falco/main' -include { MTNUCRATIO } from '../modules/nf-core/mtnucratio/main' - include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' From 31008f271df428278d9b394b2631fbbc63990946 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 21 Jul 2023 14:48:17 +0200 Subject: [PATCH 04/15] adding versions --- workflows/eager.nf | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/workflows/eager.nf b/workflows/eager.nf index 224699916..82c7545cc 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -98,8 +98,8 @@ include { MTNUCRATIO } from '../modules/n include { HOST_REMOVAL } from '../modules/local/host_removal' include { ENDORSPY } from '../modules/nf-core/endorspy/main' include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTATS_BAM_INPUT } from '../modules/nf-core/samtools/flagstat/main' -include { BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_DEPTH ; BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_BREADTH } from '../modules/nf-core/bedtools/coverage/main' -include { SAMTOOLS_VIEW_GENOME } from '../modules/local/samtools_view_genome.nf' +include { BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_DEPTH ; BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_BREADTH } from '../modules/nf-core/bedtools/coverage/main' +include { SAMTOOLS_VIEW_GENOME } from '../modules/local/samtools_view_genome.nf' include { QUALIMAP_BAMQC } from '../modules/nf-core/qualimap/bamqc/main' @@ -157,11 +157,11 @@ workflow EAGER { file(params.input) ) ch_versions = ch_versions.mix( INPUT_CHECK.out.versions ) - + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ // ! There is currently no tooling to help you write a sample sheet schema - + // // SUBWORKFLOW: Indexing of reference files // @@ -291,6 +291,7 @@ workflow EAGER { [ meta, bam ] } QUALIMAP_BAMQC(ch_qualimap_input, ch_snpcapture_bed) + ch_versions = ch_versions.mix( QUALIMAP_BAMQC.out.versions ) } // @@ -418,9 +419,9 @@ workflow EAGER { // - // MODULE: Bedtools coverage + // MODULE: Bedtools coverage // - + if ( params.run_bedtools_coverage ) { ch_anno_for_bedtools = Channel.fromPath(params.mapstats_bedtools_featurefile, checkIfExists: true).collect() @@ -435,7 +436,7 @@ workflow EAGER { SAMTOOLS_VIEW_GENOME(ch_dedupped_bams) ch_genome_for_bedtools = SAMTOOLS_VIEW_GENOME.out.genome - + BEDTOOLS_COVERAGE_BREADTH(ch_dedupped_for_bedtools, ch_genome_for_bedtools) BEDTOOLS_COVERAGE_DEPTH(ch_dedupped_for_bedtools, ch_genome_for_bedtools) @@ -443,7 +444,7 @@ workflow EAGER { ch_versions = ch_versions.mix( BEDTOOLS_COVERAGE_BREADTH.out.versions ) ch_versions = ch_versions.mix( BEDTOOLS_COVERAGE_DEPTH.out.versions ) } - + // // SUBWORKFLOW: Calculate Damage From 1c101b120f883476e7c17d4c51c3063fcfe46d67 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Sat, 22 Jul 2023 11:04:58 +0200 Subject: [PATCH 05/15] Adding multiqc --- workflows/eager.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/eager.nf b/workflows/eager.nf index 82c7545cc..de8aad794 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -291,7 +291,8 @@ workflow EAGER { [ meta, bam ] } QUALIMAP_BAMQC(ch_qualimap_input, ch_snpcapture_bed) - ch_versions = ch_versions.mix( QUALIMAP_BAMQC.out.versions ) + ch_versions = ch_versions.mix( QUALIMAP_BAMQC.out.versions ) + ch_multiqc_files = ch_multiqc_files.mix( QUALIMAP_BAMQC.out.results.collect{it[1]}.ifEmpty([]) ) } // From 7dcb5738f85eab7c1bb46f3dac636161a7e11d16 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 28 Jul 2023 10:36:37 +0200 Subject: [PATCH 06/15] moving multiqc_qualimap --- workflows/eager.nf | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/workflows/eager.nf b/workflows/eager.nf index de8aad794..439e79934 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -292,7 +292,6 @@ workflow EAGER { } QUALIMAP_BAMQC(ch_qualimap_input, ch_snpcapture_bed) ch_versions = ch_versions.mix( QUALIMAP_BAMQC.out.versions ) - ch_multiqc_files = ch_multiqc_files.mix( QUALIMAP_BAMQC.out.results.collect{it[1]}.ifEmpty([]) ) } // @@ -516,6 +515,10 @@ workflow EAGER { ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) //ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) // Replaced with custom mixing + if ( !params.skip_qualimap ) { + ch_multiqc_files = ch_multiqc_files.mix( QUALIMAP_BAMQC.out.results.collect{it[1]}.ifEmpty([]) ) + } + MULTIQC ( ch_multiqc_files.collect(), ch_multiqc_config.toList(), From 3c0877102ff5e102c1ec96c769eff8b7b7bae6a3 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 28 Jul 2023 10:43:59 +0200 Subject: [PATCH 07/15] Apply suggestions from code review Co-authored-by: James A. Fellows Yates --- nextflow.config | 1 - workflows/eager.nf | 10 +++------- 2 files changed, 3 insertions(+), 8 deletions(-) diff --git a/nextflow.config b/nextflow.config index af7ac4034..a20ae5a5e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -154,7 +154,6 @@ params { contamination_estimation_angsd_minq = 30 contamination_estimation_angsd_hapmap = "${baseDir}/assets/angsd_resources/HapMapChrX.gz" - // MtNucRatio run_mtnucratio = false mitochondrion_header = 'MT' diff --git a/workflows/eager.nf b/workflows/eager.nf index de8aad794..96c13e942 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -100,8 +100,7 @@ include { ENDORSPY } from '../modules/n include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTATS_BAM_INPUT } from '../modules/nf-core/samtools/flagstat/main' include { BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_DEPTH ; BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_BREADTH } from '../modules/nf-core/bedtools/coverage/main' include { SAMTOOLS_VIEW_GENOME } from '../modules/local/samtools_view_genome.nf' -include { QUALIMAP_BAMQC } from '../modules/nf-core/qualimap/bamqc/main' - +include { QUALIMAP_BAMQC } from '../modules/nf-core/qualimap/bamqc/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -140,15 +139,14 @@ workflow EAGER { // QualiMap if ( params.snpcapture_bed ) { - ch_snpcapture_bed = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect() + ch_snpcapture_bed = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect() } else { - ch_snpcapture_bed = [] + ch_snpcapture_bed = [] } // Contamination estimation hapmap_file = file(params.contamination_estimation_angsd_hapmap, checkIfExists:true) - // // SUBWORKFLOW: Read in samplesheet, validate and stage input files // @@ -157,7 +155,6 @@ workflow EAGER { file(params.input) ) ch_versions = ch_versions.mix( INPUT_CHECK.out.versions ) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ // ! There is currently no tooling to help you write a sample sheet schema @@ -446,7 +443,6 @@ workflow EAGER { ch_versions = ch_versions.mix( BEDTOOLS_COVERAGE_DEPTH.out.versions ) } - // // SUBWORKFLOW: Calculate Damage // From 324fd278222bbaf8fa563935997a17fb38db1fda Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 28 Jul 2023 12:22:02 +0200 Subject: [PATCH 08/15] Apply suggestions from code review Co-authored-by: James A. Fellows Yates Co-authored-by: Thiseas C. Lamnidis --- conf/modules.config | 2 +- docs/output.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4bbd59519..904e63981 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -822,7 +822,7 @@ process { withName: "QUALIMAP_BAMQC" { tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}" } publishDir = [ - path: { "${params.outdir}/mapstats/qualimap" }, + path: { "${params.outdir}/mapstats/qualimap/${meta.reference}/${meta.sample_id}/}" }, mode: params.publish_dir_mode, enabled: true ] diff --git a/docs/output.md b/docs/output.md index 33b939987..d84c9ec02 100644 --- a/docs/output.md +++ b/docs/output.md @@ -398,7 +398,7 @@ These curves will be displayed in the pipeline run's MultiQC report, however you [QualiMap](http://qualimap.bioinfo.cipf.es/) is a tool which provides statistics on the quality of the mapping of your reads to your reference genome. It allows you to assess how well covered your reference genome is by your data, both in 'fold' depth (average number of times a given base on the reference is covered by a read) and 'percentage' (the percentage of all bases on the reference genome that is covered at a given fold depth). These outputs allow you to make decision if you have enough quality data for downstream applications like genotyping, and how to adjust the parameters for those tools accordingly. -> NB: Neither fold coverage nor percent coverage on there own is sufficient to assess whether you have a high quality mapping. Abnormally high fold coverages of a smaller region such as highly conserved genes or un-removed-adapter-containing reference genomes can artificially inflate the mean coverage, yet a high percent coverage is not useful if all bases of the genome are covered at just 1x coverage. +> NB: Neither fold coverage nor percent coverage on its own is sufficient to assess whether you have a high quality mapping. Abnormally high fold coverages of a smaller region such as highly conserved genes or un-removed-adapter-containing reference genomes can artificially inflate the mean coverage, yet a high percent coverage is not useful if all bases of the genome are covered at just 1x coverage. **Note that many of the statistics from this module are displayed in the General Stats table, as they represent single values that are not plottable.** From bf50313dd74e9e8d5fef6592044e1335069696c2 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 4 Aug 2023 12:04:46 +0200 Subject: [PATCH 09/15] Adding the snpcapure to CI testing --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4df3b5a51..5437003e0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,7 @@ jobs: - "-profile test,docker --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam" - "-profile test,docker --mapping_tool bowtie2" - "-profile test,docker --skip_preprocessing" - - "-profile test_humanbam,docker --run_mtnucratio --run_contamination_estimation_angsd" + - "-profile test_humanbam,docker --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'" - "-profile test_multiref,docker" ## TODO add damage manipulation here instead once it goes multiref steps: - name: Check out pipeline code From d46a98c03664daa851addaa612acf80b0f30bf57 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 18 Aug 2023 11:56:27 +0200 Subject: [PATCH 10/15] Fixing testing gzip bed --- nextflow_schema.json | 2 +- workflows/eager.nf | 13 ++++++++++++- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index b08654252..0596e2332 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -965,7 +965,7 @@ }, "snpcapture_bed": { "type": "string", - "description": "Path to snp capture BED" + "description": "Path to snp capture in BED format." } }, "fa_icon": "fas fa-search" diff --git a/workflows/eager.nf b/workflows/eager.nf index cc7bb3e89..21816c255 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -101,6 +101,7 @@ include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTATS_BAM_INPUT } from '../modules/n include { BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_DEPTH ; BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_BREADTH } from '../modules/nf-core/bedtools/coverage/main' include { SAMTOOLS_VIEW_GENOME } from '../modules/local/samtools_view_genome.nf' include { QUALIMAP_BAMQC } from '../modules/nf-core/qualimap/bamqc/main' +include { GUNZIP as GUNZIP_SNPBED } from '../modules/nf-core/gunzip/main.nf' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -139,7 +140,17 @@ workflow EAGER { // QualiMap if ( params.snpcapture_bed ) { - ch_snpcapture_bed = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect() + ch_snpcapture_bed_gunzip = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect().map{ + file -> + meta = file.simpleName + [meta,file] + }.branch{ + meta, bed -> + forgunzip: bed[0].extension == "gz" + skip: true + } + ch_snpcapture_bed = GUNZIP_SNPBED(ch_snpcapture_bed_gunzip.forgunzip).gunzip.mix(ch_snpcapture_bed_gunzip).map{it[1]} + } else { ch_snpcapture_bed = [] } From 7017c50796ed1722c5b78d408251351c6907d1a8 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 25 Aug 2023 11:37:46 +0200 Subject: [PATCH 11/15] Adding Thiseas suggestion --- workflows/eager.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/eager.nf b/workflows/eager.nf index 21816c255..506758587 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -149,7 +149,7 @@ workflow EAGER { forgunzip: bed[0].extension == "gz" skip: true } - ch_snpcapture_bed = GUNZIP_SNPBED(ch_snpcapture_bed_gunzip.forgunzip).gunzip.mix(ch_snpcapture_bed_gunzip).map{it[1]} + ch_snpcapture_bed = GUNZIP_SNPBED(ch_snpcapture_bed_gunzip.forgunzip).gunzip.mix(ch_snpcapture_bed_gunzip.skip).map{it[1]} } else { ch_snpcapture_bed = [] From b99321c372d9fc8333699ba9988871adee73b5ba Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 25 Aug 2023 12:50:08 +0200 Subject: [PATCH 12/15] Apply suggestions from code review Co-authored-by: Thiseas C. Lamnidis --- nextflow_schema.json | 2 +- workflows/eager.nf | 17 ++++++++++------- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 0596e2332..904c7ef61 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -965,7 +965,7 @@ }, "snpcapture_bed": { "type": "string", - "description": "Path to snp capture in BED format." + "description": "Path to snp capture in BED format. Provided file can also be gzipped." } }, "fa_icon": "fas fa-search" diff --git a/workflows/eager.nf b/workflows/eager.nf index 506758587..8024f354b 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -140,15 +140,18 @@ workflow EAGER { // QualiMap if ( params.snpcapture_bed ) { - ch_snpcapture_bed_gunzip = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect().map{ - file -> - meta = file.simpleName - [meta,file] - }.branch{ - meta, bed -> + ch_snpcapture_bed_gunzip = Channel.fromPath( params.snpcapture_bed, checkIfExists: true ) + .collect() + .map { + file -> + meta = file.simpleName + [meta,file] + } + .branch { + meta, bed -> forgunzip: bed[0].extension == "gz" skip: true - } + } ch_snpcapture_bed = GUNZIP_SNPBED(ch_snpcapture_bed_gunzip.forgunzip).gunzip.mix(ch_snpcapture_bed_gunzip.skip).map{it[1]} } else { From 5bf28e52207d2f6b75f1fb88e353581b26776b7f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Sep 2023 15:16:27 +0000 Subject: [PATCH 13/15] Template update for nf-core/tools version 2.10 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 4 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcments.yml | 68 +++++++++ CITATIONS.md | 2 +- CODE_OF_CONDUCT.md | 133 ++++++++++++++---- README.md | 21 +-- assets/multiqc_config.yml | 4 +- conf/modules.config | 9 ++ docs/output.md | 5 +- docs/usage.md | 16 ++- lib/NfcoreTemplate.groovy | 16 +++ lib/WorkflowEager.groovy | 2 +- main.nf | 3 + modules.json | 6 +- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 8 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 7 +- nextflow_schema.json | 15 -- workflows/eager.nf | 1 + 21 files changed, 251 insertions(+), 76 deletions(-) create mode 100644 .github/workflows/release-announcments.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ea27a5843..4ecfbfe33 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,6 +2,7 @@ "name": "nfcore", "image": "nfcore/gitpod:latest", "remoteUser": "gitpod", + "runArgs": ["--privileged"], // Configure tool-specific properties. "customizations": { diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 7f42e77a6..fa933e118 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +9,9 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -> If you need help using or modifying nf-core/eager then the best place to ask is on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/eager then the best place to ask is on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc3..b8bdd2143 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml new file mode 100644 index 000000000..6ad339277 --- /dev/null +++ b/.github/workflows/release-announcments.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy + + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.0.2 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/CITATIONS.md b/CITATIONS.md index 767e7e791..41dfea017 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052f1..c089ec78c 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/README.md b/README.md index f39453220..7dab64c65 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # ![nf-core/eager](docs/images/nf-core-eager_logo_light.png#gh-light-mode-only) ![nf-core/eager](docs/images/nf-core-eager_logo_dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/eager/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/nf-core/eager/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/eager/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/eager/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/eager/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/eager/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -29,10 +30,11 @@ ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +:::note +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +with `-profile test` before running the workflow on actual data. +:::