diff --git a/assets/schema_input.json b/assets/schema_input.json index acdf9dcb7..52e4f06bc 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -35,27 +35,33 @@ }, "replicate": { "type": "integer", - "errorMessage": "Replicate id not an integer!", + "minimum": 1, + "errorMessage": "Replicate id must be a positive integer!", "meta": ["replicate"] }, "antibody": { "type": "string", - "pattern": "^\\S+$", - "errorMessage": "Antibody entry cannot contain spaces", + "pattern": "^[\\w.-]+$", + "errorMessage": "Antibody entry must contain only alphanumeric characters, dots, and hyphens", "meta": ["antibody"] }, "control": { "type": "string", - "pattern": "^\\S+$", - "errorMessage": "Control entry cannot contain spaces", + "pattern": "^[\\w.-]+$", + "errorMessage": "Control entry must contain only alphanumeric characters, dots, and hyphens", "meta": ["control"] }, "control_replicate": { "type": "integer", - "errorMessage": "Replicate id not an integer!", + "minimum": 1, + "errorMessage": "Control replicate id must be a positive integer!", "meta": ["control_replicate"] } }, - "required": ["sample", "fastq_1"] + "required": ["sample", "fastq_1"], + "dependentRequired": { + "antibody": ["control"], + "control": ["antibody"] + } } } diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index d34f42ed0..000000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,247 +0,0 @@ -#!/usr/bin/env python3 - -import os -import sys -import errno -import argparse -import re - - -def parse_args(args=None): - Description = "Reformat nf-core/chipseq samplesheet file and check its contents." - Epilog = "Example usage: python check_samplesheet.py " - - parser = argparse.ArgumentParser(description=Description, epilog=Epilog) - parser.add_argument("FILE_IN", help="Input samplesheet file.") - parser.add_argument("FILE_OUT", help="Output file.") - return parser.parse_args(args) - - -def make_dir(path): - if len(path) > 0: - try: - os.makedirs(path) - except OSError as exception: - if exception.errno != errno.EEXIST: - raise exception - - -def print_error(error, context="Line", context_str=""): - error_str = "ERROR: Please check samplesheet -> {}".format(error) - if context != "" and context_str != "": - error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format( - error, context.strip(), context_str.strip() - ) - print(error_str) - sys.exit(1) - - -def check_samplesheet(file_in, file_out): - """ - This function checks that the samplesheet follows the following structure: - sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate - SPT5_T0,SRR1822153_1.fastq.gz,SRR1822153_2.fastq.gz,SPT5,1,SPT5_INPUT,1 - SPT5_T0,SRR1822154_1.fastq.gz,SRR1822154_2.fastq.gz,SPT5,2,SPT5_INPUT,2 - SPT5_INPUT,SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz,SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz,1,,, - SPT5_INPUT,SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz,SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz,2,,, - For an example see: - https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.1/samplesheet_test.csv - """ - - sample_mapping_dict = {} - with open(file_in, "r", encoding="utf-8-sig") as fin: - ## Check header - MIN_COLS = 3 - HEADER = ["sample", "fastq_1", "fastq_2", "replicate", "antibody", "control", "control_replicate"] - header = [x.strip('"') for x in fin.readline().strip().split(",")] - if header[: len(HEADER)] != HEADER: - print(f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}") - sys.exit(1) - - ## Check sample entries - for line_number, line in enumerate(fin, start=1): - if line.strip(): - lspl = [x.strip().strip('"') for x in line.strip().split(",")] - - # Check valid number of columns per row - if len(lspl) < len(HEADER): - print_error( - "Invalid number of columns (found = {}, minimum = {})!".format(len(lspl),len(HEADER)), - "Line {}".format(line_number), - line, - ) - num_cols = len([x for x in lspl[: len(HEADER)] if x]) - if num_cols < MIN_COLS: - print_error( - "Invalid number of populated columns (found = {}, minimum = {})!".format(num_cols,MIN_COLS), - "Line {}".format(line_number), - line, - ) - - ## Check sample name entries - sample, fastq_1, fastq_2, replicate, antibody, control, control_replicate = lspl[: len(HEADER)] - if sample.find(" ") != -1: - print(f"WARNING: Spaces have been replaced by underscores for sample: {sample}") - sample = sample.replace(" ", "_") - if not sample: - print_error("Sample entry has not been specified!", "Line {}".format(line_number), line) - if not re.match(r"^[a-zA-Z0-9_.-]+$", sample): - print_error( - "Sample name contains invalid characters! Only alphanumeric characters, underscores, dots and dashes are allowed.", - "Line {}".format(line_number), - line, - ) - - ## Check FastQ file extension - for fastq in [fastq_1, fastq_2]: - if fastq: - if fastq.find(" ") != -1: - print_error("FastQ file contains spaces!", "Line {}".format(line_number), line) - if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"): - print_error( - "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!", - "Line {}".format(line_number), - line, - ) - - ## Check replicate column is integer - if not replicate.isdecimal(): - print_error("Replicate id not an integer!", "Line {}".format(line_number), line) - sys.exit(1) - - ## Check antibody and control columns have valid values - if antibody: - if antibody.find(" ") != -1: - print(f"WARNING: Spaces have been replaced by underscores for antibody: {antibody}") - antibody = antibody.replace(" ", "_") - if not control: - print_error( - "Both antibody and control columns must be specified!", - "Line {}".format(line_number), - line, - ) - - if control: - if control.find(" ") != -1: - print(f"WARNING: Spaces have been replaced by underscores for control: {control}") - control = control.replace(" ", "_") - if not control_replicate.isdecimal(): - print_error("Control replicate id not an integer!", "Line {}".format(line_number), line) - sys.exit(1) - control = "{}_REP{}".format(control, control_replicate) - if not antibody: - print_error( - "Both antibody and control columns must be specified!", - "Line {}".format(line_number), - line, - ) - - ## Auto-detect paired-end/single-end - sample_info = [] ## [single_end, fastq_1, fastq_2, replicate, antibody, control] - ## Paired-end short reads - if sample and fastq_1 and fastq_2: - sample_info = ["0", fastq_1, fastq_2, replicate, antibody, control] - ## Single-end short reads - elif sample and fastq_1 and not fastq_2: - sample_info = ["1", fastq_1, fastq_2, replicate, antibody, control] - else: - print_error("Invalid combination of columns provided!", "Line {}".format(line_number), line) - - ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, replicate, antibody, control ]]} - replicate = int(replicate) - sample_info = sample_info + lspl[len(HEADER) :] - if sample not in sample_mapping_dict: - sample_mapping_dict[sample] = {} - if replicate not in sample_mapping_dict[sample]: - sample_mapping_dict[sample][replicate] = [sample_info] - else: - if sample_info in sample_mapping_dict[sample][replicate]: - print_error("Samplesheet contains duplicate rows!", "Line {}".format(line_number), line) - else: - sample_mapping_dict[sample][replicate].append(sample_info) - - ## Write validated samplesheet with appropriate columns - if len(sample_mapping_dict) > 0: - out_dir = os.path.dirname(file_out) - make_dir(out_dir) - with open(file_out, "w") as fout: - fout.write( - ",".join( - [ - "sample", - "single_end", - "fastq_1", - "fastq_2", - "replicate", - "antibody", - "control", - ] - ) - + "\n" - ) - for sample in sorted(sample_mapping_dict.keys()): - ## Check that replicate ids are in format 1.. - uniq_rep_ids = sorted(list(set(sample_mapping_dict[sample].keys()))) - if len(uniq_rep_ids) != max(uniq_rep_ids) or 1 != min(uniq_rep_ids): - print_error( - "Replicate ids must start with 1..!", - "Sample", - "{}, replicate ids: {}".format(sample, ",".join([str(x) for x in uniq_rep_ids])), - ) - sys.exit(1) - - ## Check that multiple replicates are of the same datatype i.e. single-end / paired-end - if not all( - x[0][0] == sample_mapping_dict[sample][1][0][0] for x in sample_mapping_dict[sample].values() - ): - print_error( - f"Multiple replicates of a sample must be of the same datatype i.e. single-end or paired-end!", - "Sample", - sample, - ) - - for replicate in sorted(sample_mapping_dict[sample].keys()): - ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - if not all( - x[0] == sample_mapping_dict[sample][replicate][0][0] - for x in sample_mapping_dict[sample][replicate] - ): - print_error( - f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!", - "Sample", - sample, - ) - - for idx, val in enumerate(sample_mapping_dict[sample][replicate]): - control = "_REP".join(val[-1].split("_REP")[:-1]) - control_replicate = val[-1].split("_REP")[-1] - if control and ( - control not in sample_mapping_dict.keys() - or int(control_replicate) not in sample_mapping_dict[control].keys() - ): - print_error( - f"Control identifier and replicate has to match a provided sample identifier and replicate!", - "Control", - val[-1], - ) - - ## Write to file - for idx in range(len(sample_mapping_dict[sample][replicate])): - fastq_files = sample_mapping_dict[sample][replicate][idx] - sample_id = "{}_REP{}_T{}".format(sample, replicate, idx + 1) - if len(fastq_files) == 1: - fout.write(",".join([sample_id] + fastq_files) + ",\n") - else: - fout.write(",".join([sample_id] + fastq_files) + "\n") - - else: - print_error(f"No entries to process!", "Samplesheet: {file_in}") - - -def main(args=None): - args = parse_args(args) - check_samplesheet(args.FILE_IN, args.FILE_OUT) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/main.nf b/main.nf index 26bdbbc4d..b92c63976 100755 --- a/main.nf +++ b/main.nf @@ -48,6 +48,9 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_chip // workflow NFCORE_CHIPSEQ { + take: + samplesheet // channel: pre-validated samplesheet data from nf-schema + main: ch_versions = Channel.empty() @@ -71,10 +74,8 @@ workflow NFCORE_CHIPSEQ { // // WORKFLOW: Run nf-core/chipseq workflow // - ch_samplesheet = Channel.value(file(params.input, checkIfExists: true)) - CHIPSEQ( - ch_samplesheet, + samplesheet, ch_versions, PREPARE_GENOME.out.fasta, PREPARE_GENOME.out.fai, @@ -116,7 +117,9 @@ workflow { // // WORKFLOW: Run main workflow // - NFCORE_CHIPSEQ ( ) + NFCORE_CHIPSEQ ( + PIPELINE_INITIALISATION.out.samplesheet + ) // // SUBWORKFLOW: Run completion tasks diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf index 620529ce0..5f285cd8b 100644 --- a/modules/local/multiqc.nf +++ b/modules/local/multiqc.nf @@ -15,37 +15,37 @@ process MULTIQC { path "trimgalore/fastqc/*" path "trimgalore/*" - path "alignment/library/*" - path "alignment/library/*" - path "alignment/library/*" + path "alignment/library/samtools_stats/*" + path "alignment/library/samtools_flagstat/*" + path "alignment/library/samtools_idxstats/*" - path "alignment/merged_library/unfiltered/*" - path "alignment/merged_library/unfiltered/*" - path "alignment/merged_library/unfiltered/*" + path "alignment/merged_library/unfiltered/samtools_stats/*" + path "alignment/merged_library/unfiltered/samtools_flagstat/*" + path "alignment/merged_library/unfiltered/samtools_idxstats/*" path "alignment/merged_library/unfiltered/picard_metrics/*" - path "alignment/merged_library/filtered/*" - path "alignment/merged_library/filtered/*" - path "alignment/merged_library/filtered/*" + path "alignment/merged_library/filtered/samtools_stats/*" + path "alignment/merged_library/filtered/samtools_flagstat/*" + path "alignment/merged_library/filtered/samtools_idxstats/*" path "alignment/merged_library/filtered/picard_metrics/*" path "preseq/*" - path "deeptools/*" - path "deeptools/*" + path "deeptools/plotprofile/*" + path "deeptools/plotfingerprint/*" - path "phantompeakqualtools/*" - path "phantompeakqualtools/*" - path "phantompeakqualtools/*" - path "phantompeakqualtools/*" + path "phantompeakqualtools/spp/*" + path "phantompeakqualtools/nsc/*" + path "phantompeakqualtools/rsc/*" + path "phantompeakqualtools/correlation/*" - path "macs3/peaks/*" - path "macs3/peaks/*" + path "macs3/peaks/frip/*" + path "macs3/peaks/count/*" path "macs3/annotation/*" path "macs3/featurecounts/*" - path "deseq2/*" - path "deseq2/*" + path "deseq2/pca/*" + path "deseq2/clustering/*" output: path "*multiqc_report.html", emit: report diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 216e9fb78..000000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,32 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/ - def args = task.ext.args ?: '' - """ - check_samplesheet.py \\ - $samplesheet \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 40e20bd1e..000000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,52 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - seq_center // string: sequencing center for read group - - main: - SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it, seq_center) } - .set { reads } - - emit: - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row, String seq_center) { - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - meta.antibody = row.antibody - meta.control = row.control - - def read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id - ~/_T\d+$/}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\'" - if (seq_center) { - read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id - ~/_T\d+$/}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\\tCN:${seq_center}\'" - } - meta.read_group = read_group - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} diff --git a/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf index 2f4aeaa6a..8ebc93ceb 100644 --- a/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf @@ -78,6 +78,32 @@ workflow PIPELINE_INITIALISATION { versions = ch_versions } +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + SUBWORKFLOW FOR INPUT CHECK +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// Process pre-validated samplesheet data and get read channels +// +workflow INPUT_CHECK { + take: + samplesheet // channel: pre-validated samplesheet data from nf-schema + seq_center // string: sequencing center for read group + + main: + ch_versions = Channel.empty() + + samplesheet + .map { create_fastq_channel(it, seq_center) } + .set { reads } + + emit: + reads // channel: [ val(meta), [ reads ] ] + versions = ch_versions // channel: [ versions.yml ] +} + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION @@ -256,3 +282,73 @@ def macsGsizeWarn(log) { " Explicitly provide '--macs_gsize macs3_genome_size' to change this behaviour.\n" + "===================================================================================" } + +// +// Validate samplesheet rows and apply custom logic +// +def validateSamplesheetRow(LinkedHashMap row) { + // Check for spaces in sample name and replace with warnings + if (row.sample && row.sample.toString().contains(' ')) { + log.warn "Sample name '${row.sample}' contains spaces. These will be replaced with underscores in output files." + row.sample = row.sample.toString().replace(' ', '_') + } + + // Check for spaces in antibody field and warn + if (row.antibody && row.antibody.toString().contains(' ')) { + log.warn "Antibody name '${row.antibody}' contains spaces. Consider using underscores or hyphens instead." + row.antibody = row.antibody.toString().replace(' ', '_') + } + + // Check for spaces in control field and warn + if (row.control && row.control.toString().contains(' ')) { + log.warn "Control name '${row.control}' contains spaces. Consider using underscores or hyphens instead." + row.control = row.control.toString().replace(' ', '_') + } + + // Compute single_end based on fastq_2 field + row.single_end = (row.fastq_2 == null || row.fastq_2.toString().trim() == "") + + return row +} + +// +// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] +// +def create_fastq_channel(data_list, String seq_center) { + // nf-schema returns: [meta, fastq_1, fastq_2, replicate, antibody, control, control_replicate] + // Extract the parts + def meta_from_schema = data_list[0] + def fastq_1 = data_list[1] + def fastq_2 = data_list[2] + def replicate = meta_from_schema.replicate ?: 1 + def antibody = meta_from_schema.antibody ?: '' + def control = meta_from_schema.control ?: '' + def control_replicate = meta_from_schema.control_replicate ?: 1 + + // Debug output can be enabled for troubleshooting + // log.info "DEBUG: Processing sample - original_id: ${meta_from_schema.id}, replicate: ${replicate}, control: '${control}', control_replicate: ${control_replicate}" + + def meta = [:] + meta.id = "${meta_from_schema.id}_rep${replicate}" + meta.single_end = (fastq_2 == null || fastq_2.toString().trim() == '' || fastq_2 instanceof List && fastq_2.isEmpty()) + meta.antibody = antibody + // Transform control reference to include replicate suffix for proper IP/control pairing + meta.control = control ? "${control}_rep${control_replicate}" : control + meta.replicate = replicate + meta.control_replicate = control_replicate + + def read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id - ~/_T\d+$/}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\'" + if (seq_center) { + read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id - ~/_T\d+$/}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\\tCN:${seq_center}\'" + } + meta.read_group = read_group + + // File paths are already validated by nf-schema + def fastq_meta = [] + if (meta.single_end) { + fastq_meta = [ meta, [ file(fastq_1) ] ] + } else { + fastq_meta = [ meta, [ file(fastq_1), file(fastq_2) ] ] + } + return fastq_meta +} diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap index 42a9e46f5..89a9a4c8d 100644 --- a/tests/bowtie2.nf.test.snap +++ b/tests/bowtie2.nf.test.snap @@ -1,11 +1,8 @@ { "bowtie2": { "content": [ - 215, + 187, { - "ANNOTATE_BOOLEAN_PEAKS": { - "sed": 4.7 - }, "BAMTOOLS_FILTER": { "bamtools": "2.5.2", "samtools": "1.15.1" @@ -30,48 +27,24 @@ "DEEPTOOLS_COMPUTEMATRIX": { "deeptools": "3.5.5" }, - "DEEPTOOLS_PLOTFINGERPRINT": { - "deeptools": "3.5.5" - }, "DEEPTOOLS_PLOTHEATMAP": { "deeptools": "3.5.5" }, "DEEPTOOLS_PLOTPROFILE": { "deeptools": "3.5.5" }, - "DESEQ2_QC": { - "bioconductor-deseq2": "1.28.0", - "r-base": "4.0.3" - }, "FASTQC": { "fastqc": "0.12.1" }, - "FRIP_SCORE": { - "bedtools": "2.30.0", - "samtools": "1.15.1" - }, "GENOME_BLACKLIST_REGIONS": { "bedtools": "2.30.0" }, "GTF2BED": { "perl": "5.26.2" }, - "HOMER_ANNOTATEPEAKS": { - "homer": 4.11 - }, "IGV": { "python": "3.8.3" }, - "MACS3_CALLPEAK": { - "macs3": "3.0.1" - }, - "MACS3_CONSENSUS": { - "python": "3.10.0", - "r-base": "4.1.1" - }, - "MULTIQC_CUSTOM_PEAKS": { - "sed": 4.7 - }, "PHANTOMPEAKQUALTOOLS": { "phantompeakqualtools": "1.2.2" }, @@ -84,15 +57,6 @@ "PICARD_MERGESAMFILES": { "picard": "3.2.0-1-g3948afb6b" }, - "PLOT_HOMER_ANNOTATEPEAKS": { - "r-base": "4.0.3" - }, - "PLOT_MACS3_QC": { - "r-base": "4.0.3" - }, - "SAMPLESHEET_CHECK": { - "python": "3.8.3" - }, "SAMTOOLS_FLAGSTAT": { "samtools": "1.22.1" }, @@ -108,9 +72,6 @@ "SAMTOOLS_STATS": { "samtools": 1.2 }, - "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" - }, "TRIMGALORE": { "cutadapt": 3.4, "trimgalore": "0.6.7" @@ -125,285 +86,213 @@ [ "bowtie2", "bowtie2/merged_library", - "bowtie2/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam", - "bowtie2/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam.bai", - "bowtie2/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam", - "bowtie2/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam.bai", - "bowtie2/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam", - "bowtie2/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam.bai", - "bowtie2/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam", - "bowtie2/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam.bai", - "bowtie2/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam", - "bowtie2/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam.bai", - 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"fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3", - "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c", - "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2", - "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678", - "fastqc_sequence_length_distribution_plot.yaml:md5,f1d36d9bed4b85e0ae349b514ab788fc", + "fastqc-status-check-heatmap.yaml:md5,735618bef1e56ee95417ad4aa05983ce", + "fastqc_adapter_content_plot.yaml:md5,bcbd28c1aa6bc4c446d8ab7ff3344356", + "fastqc_per_base_n_content_plot.yaml:md5,435ffbb377c0729249c316c35aa5a08f", + "fastqc_per_base_sequence_quality_plot.yaml:md5,eea9f7351dd013df7712fd00d0ac2241", + "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,5f1ab6f624e5660428725804a2edc75c", + "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,7adfd2616e1098e58bab86ceed7434bf", + "fastqc_per_sequence_quality_scores_plot.yaml:md5,d6183307cf87d4a09281960c7ba8607a", + "fastqc_sequence_counts_plot.yaml:md5,3543abf15a4c45007e7560eb020aacc8", + "fastqc_sequence_duplication_levels_plot.yaml:md5,2cb3fb1353d1de2bf5def6c2f7faa356", + "fastqc_sequence_length_distribution_plot.yaml:md5,e0814db7689c1782b253702b1109ce9e", "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d", - "featureCounts_assignment_plot.yaml:md5,83f65e024cdcf840199ff56dfdbbc0fc", - "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3", - "multiqc_cutadapt.yaml:md5,25f32008ccf0041ac74bb82d744d6eda", - "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9", - "multiqc_fastqc_1.yaml:md5,dd7981fa28827b895ef844011053eeff", - "multiqc_featurecounts.yaml:md5,b04c61a636508a406a40d532c3841474", - "multiqc_frip_score.yaml:md5,ac21032eb4978f8bc2ef2d03dfc7c04c", - "multiqc_nsc_coefficient.yaml:md5,63db816351d46b1420aa35dca04a4a3f", - "multiqc_peak_annotation.yaml:md5,eed4fb1ce72c9dfcf28b33143a5f63c5", - "multiqc_peak_count.yaml:md5,b595892dcd65c4f233597c17b0d982f1", - "multiqc_phantompeakqualtools.yaml:md5,ddadca49d172a77ea491675930155413", - "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,86347cb87e66b56dfa591568ebfd4c24", - "multiqc_picard-1_insertSize.yaml:md5,e0fb94ddfce5be120711660801850972", - "multiqc_picard-1_quality_by_cycle.yaml:md5,2478f6aac43166b2c6b3cc653288579e", - "multiqc_picard-1_quality_score_distribution.yaml:md5,63f6a752be596fb6ad1a8b1c8bbdf17a", - "multiqc_picard_baseContent.yaml:md5,8fe24fbc195b032c064f9267349a8826", - "multiqc_picard_dups.yaml:md5,daf7f91937e15046c525c6032813bc75", - "multiqc_rsc_coefficient.yaml:md5,70d442b344556b9fd6ab591d38423004", - "multiqc_samtools_flagstat.yaml:md5,7f49f4aeeaa0b33a6a56403ef4e511ba", - "multiqc_samtools_flagstat_1.yaml:md5,e7826d97bcb600953a58814996f864e6", - "multiqc_samtools_flagstat_2.yaml:md5,42a4d5406638556c65e9060f9497b960", - "multiqc_samtools_idxstats.yaml:md5,0d1f6bbff844c69680de2e3a0b744b8e", - "multiqc_samtools_idxstats_1.yaml:md5,41b238a7390ff63af594d4301f734900", - "multiqc_samtools_idxstats_2.yaml:md5,9aa46ef39c0d1c9a59ad186f3939955f", - "multiqc_samtools_stats.yaml:md5,c1f753728b7d0d969f1de706989508ea", - "multiqc_samtools_stats_1.yaml:md5,ac39dbae7578b4fc13bf2753d9f2d2eb", - "multiqc_samtools_stats_2.yaml:md5,1bb38f88e3cf993ffd1c1eca67965f48", - "multiqc_strand_shift_correlation.yaml:md5,87ce7906a3297afe5f5d73fe6e6d86ca", - "picard-1_alignment_readlength_plot.yaml:md5,ef8322029669a340b33c3efe78c5df94", - "picard-1_alignment_summary_Aligned_Bases.yaml:md5,0f3082cdd9d84f49658e02ab83ecd123", - "picard-1_alignment_summary_Aligned_Reads.yaml:md5,12710ac1215929e04b124952d9ce9ac3", + "multiqc_citations.yaml:md5,c4cdebc20cfc52eb2eee741a36323b3e", + "multiqc_cutadapt.yaml:md5,74b42e87a78ac23b716acec17b3f97b6", + "multiqc_fastqc.yaml:md5,33eb21cad7eafc05b0646954fdeb3e99", + "multiqc_fastqc_1.yaml:md5,7cd54ec9c1c4f5974bd7c3289971a9d5", + "multiqc_nsc_coefficient.yaml:md5,9c95673dcd8580c448141a20cc728453", + "multiqc_phantompeakqualtools.yaml:md5,9da19ff263aa845ca66568815cc0ed18", + "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,48b38e029b5eaadbc3d08ba897a6c7a9", + "multiqc_picard-1_insertSize.yaml:md5,f5cfe3581c78753943bf42545a68dbe0", + "multiqc_picard-1_quality_by_cycle.yaml:md5,35c3a3c3ef6ee7994c9f9369333dec90", + "multiqc_picard-1_quality_score_distribution.yaml:md5,25c8c34010db7ad2021270d3c93cd199", + "multiqc_picard_baseContent.yaml:md5,66f5e6ca93670f5cb99de8743e48b732", + "multiqc_picard_dups.yaml:md5,9735671bfd1932256b2e027d01189773", + "multiqc_rsc_coefficient.yaml:md5,4b6e9f16043d36e7452db3546ccd673f", + "multiqc_samtools_flagstat.yaml:md5,f817d8d87848a49159e95ca882a6d573", + "multiqc_samtools_flagstat_1.yaml:md5,68ee2c814745f5df3b8cd85a598989d4", + "multiqc_samtools_flagstat_2.yaml:md5,a06647792974b524d0e6d98dca338e7b", + "multiqc_samtools_idxstats.yaml:md5,13b7747b9ffb417f4d65a28169fa6723", + "multiqc_samtools_idxstats_1.yaml:md5,13b7747b9ffb417f4d65a28169fa6723", + "multiqc_samtools_idxstats_2.yaml:md5,3d6b7af675d81084de7d64d5e0608f69", + "multiqc_samtools_stats.yaml:md5,4ebe54e103dc7df15005417dadefc009", + "multiqc_samtools_stats_1.yaml:md5,04e2acba705ad0fcd6846c6daf119aec", + "multiqc_samtools_stats_2.yaml:md5,fdedfe3725427d54edeab16dd9ffb127", + "multiqc_strand_shift_correlation.yaml:md5,5fb944ecf420574f65b5607a56817e74", + "picard-1_alignment_readlength_plot.yaml:md5,fb28849f04b9854d46f25c18844d61a3", + "picard-1_alignment_summary_Aligned_Bases.yaml:md5,b14974b5d766b516fe5590d75926c483", + "picard-1_alignment_summary_Aligned_Reads.yaml:md5,c68d3a6bd9718e4cb9104c04a9a37d94", "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", - "picard-1_histogram_1.yaml:md5,2478f6aac43166b2c6b3cc653288579e", - "picard-1_histogram_2.yaml:md5,63f6a752be596fb6ad1a8b1c8bbdf17a", - "picard-1_insert_size_Counts.yaml:md5,8fcef0700ff63df7dbb2a0594f3294a9", - "picard-1_insert_size_Percentages.yaml:md5,ba621b3cb07eb930b769e24461a62482", - "picard-1_quality_by_cycle.yaml:md5,0432b05602d754b5f03b34c15058ed6f", - "picard-1_quality_score_distribution.yaml:md5,426e031acc10eeb8b7977401ed731dfa", - "picard_base_distribution_by_cycle__Adenine.yaml:md5,0ad2885a20e408e41c3515afecdd6ea9", - "picard_base_distribution_by_cycle__Cytosine.yaml:md5,3e6dbfb300937eabb098c65071597abd", - "picard_base_distribution_by_cycle__Guanine.yaml:md5,71b8c3f5ced0393f3b4a2dac8ee53402", - "picard_base_distribution_by_cycle__Thymine.yaml:md5,05ba2b40801888464d8e17e349387d4f", - "picard_base_distribution_by_cycle__Undetermined.yaml:md5,ecd12bd2e8698c090f06e6c6bcf37188", - "picard_deduplication.yaml:md5,f0123e6449274c09a0158657b549d861", + "picard-1_histogram_1.yaml:md5,35c3a3c3ef6ee7994c9f9369333dec90", + "picard-1_histogram_2.yaml:md5,25c8c34010db7ad2021270d3c93cd199", + "picard-1_insert_size_Counts.yaml:md5,594d8f5a2b0090402141b4b3c35de44f", + "picard-1_insert_size_Percentages.yaml:md5,147514a0943453ed38c4ae7404f49d3a", + "picard-1_quality_by_cycle.yaml:md5,2d81004ef1e2aac8ec3edfbc54244f55", + "picard-1_quality_score_distribution.yaml:md5,c213f90c580f7b016aadeee3d649dbae", + "picard_base_distribution_by_cycle__Adenine.yaml:md5,ef8a06a235be12a0a87de62d05c53efb", + "picard_base_distribution_by_cycle__Cytosine.yaml:md5,cd7d49ba79add43d8baf49e88d71b8bd", + "picard_base_distribution_by_cycle__Guanine.yaml:md5,a225cfbd0960208cd7a0770c57ab2ffd", + "picard_base_distribution_by_cycle__Thymine.yaml:md5,6467b656d5cf35c4ec8e0475cdad1ba2", + "picard_base_distribution_by_cycle__Undetermined.yaml:md5,ff257ee984e936dc7a667903a1b57910", + "picard_deduplication.yaml:md5,3d4744bc84f79e288a1c41f3ee5e3dd4", "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11", "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11", - "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,caebb683ef834e2dbfaf09a4e6751c69", - "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,92202e45b98fe15ee8966f7e85af1eb6", - "samtools-flagstat-dp_Percentage_of_total.yaml:md5,f0e636f2e22d6b7b7df0e3e22eb99e0c", - "samtools-flagstat-dp_Read_counts-1.yaml:md5,3cf4c572a179d508f53c4838f8e89de7", - "samtools-flagstat-dp_Read_counts-2.yaml:md5,d52e3e0c02a392cc4939c78dd5cb286b", - "samtools-flagstat-dp_Read_counts.yaml:md5,f278c8953daf3de4c73515f56da4d880", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,234a3bf875eb9fd93b3d43b11edc9e59", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,d1777af033fa122b9ffd86e2d165e299", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,7dbbc39984c5dc6421e68711d9f0732c", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,b7266c4e8bc759932521d0abeefccf8f", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,9e69299aa94e930736eb6d58a99e32ab", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,5823a0a1231681d8887007bd2659ee8e", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,df06db1e3a0e492bdbcef799730c2cd9", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,b210ce5a055931fd94328750454df24d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,f594898789d8f354ce7720e5cbdcb1d3", - "samtools-stats-dp.yaml:md5,a17797e8a52aff0c17051735099629fe", - "samtools_alignment_plot.yaml:md5,21e19a3581f28089acffd00121442ffc", - "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" + "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,20f1147560cf3be7cb851b4db3aa4f76", + "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,2d4f66069e759db7af0d387611571c19", + "samtools-flagstat-dp_Percentage_of_total.yaml:md5,97a0b6ea8a829369f494b872aef162f6", + "samtools-flagstat-dp_Read_counts-1.yaml:md5,17c6bed2b5af8ea66ab8a26d3bd9dcf7", + "samtools-flagstat-dp_Read_counts-2.yaml:md5,726660cc8b498a6733b912cbb6a1dafd", + "samtools-flagstat-dp_Read_counts.yaml:md5,e948798f697f7fb25c0c883c1aa87f78", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,19ac144f0b033d31553201e6d91c5d0f", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,de2445c36acc5085a03876060047ac9e", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,19ac144f0b033d31553201e6d91c5d0f", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,60056940f639e2e5a071c1b2bf2b464f", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,5cd09a83a7fb568e9f87fac109fa72d5", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,60056940f639e2e5a071c1b2bf2b464f", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,bc79380184b30076747170236e8e3123", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,0b0ca9f371c0a0357331bab2e73f885d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,bc79380184b30076747170236e8e3123", + "samtools-stats-dp.yaml:md5,6c10b4990fe6293e90690af7c02e08cf", + "samtools_alignment_plot.yaml:md5,918080c480e7ac964e452f6435f85c1a" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-17T13:11:14.489285555" + "timestamp": "2025-09-18T15:53:52.511943" }, "bowtie2 with stub": { "content": [ - 20 + 19 ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-04T20:19:29.013062" + "timestamp": "2025-09-18T15:54:17.66561" } -} +} \ No newline at end of file diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap index 2fd20e1c5..2fea52ed5 100644 --- a/tests/chromap.nf.test.snap +++ b/tests/chromap.nf.test.snap @@ -1,11 +1,8 @@ { "chromap": { "content": [ - 215, + 187, { - "ANNOTATE_BOOLEAN_PEAKS": { - "sed": 4.7 - }, "BAMTOOLS_FILTER": { "bamtools": "2.5.2", "samtools": "1.15.1" @@ -29,48 +26,24 @@ "DEEPTOOLS_COMPUTEMATRIX": { "deeptools": "3.5.5" }, - "DEEPTOOLS_PLOTFINGERPRINT": { - "deeptools": "3.5.5" - }, "DEEPTOOLS_PLOTHEATMAP": { "deeptools": "3.5.5" }, "DEEPTOOLS_PLOTPROFILE": { "deeptools": "3.5.5" }, - "DESEQ2_QC": { - "bioconductor-deseq2": "1.28.0", - "r-base": "4.0.3" - }, "FASTQC": { "fastqc": "0.12.1" }, - "FRIP_SCORE": { - "bedtools": "2.30.0", - "samtools": "1.15.1" - }, "GENOME_BLACKLIST_REGIONS": { "bedtools": "2.30.0" }, "GTF2BED": { "perl": "5.26.2" }, - "HOMER_ANNOTATEPEAKS": { - "homer": 4.11 - }, "IGV": { "python": "3.8.3" }, - "MACS3_CALLPEAK": { - "macs3": "3.0.1" - }, - "MACS3_CONSENSUS": { - "python": "3.10.0", - "r-base": "4.1.1" - }, - "MULTIQC_CUSTOM_PEAKS": { - "sed": 4.7 - }, "PHANTOMPEAKQUALTOOLS": { "phantompeakqualtools": "1.2.2" }, @@ -83,15 +56,6 @@ "PICARD_MERGESAMFILES": { "picard": "3.2.0-1-g3948afb6b" }, - "PLOT_HOMER_ANNOTATEPEAKS": { - "r-base": "4.0.3" - }, - "PLOT_MACS3_QC": { - "r-base": "4.0.3" - }, - "SAMPLESHEET_CHECK": { - "python": "3.8.3" - }, "SAMTOOLS_FLAGSTAT": { "samtools": "1.22.1" }, @@ -107,9 +71,6 @@ "SAMTOOLS_STATS": { "samtools": 1.2 }, - "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" - }, "TRIMGALORE": { "cutadapt": 3.4, "trimgalore": "0.6.7" @@ -124,285 +85,213 @@ [ "chromap", "chromap/merged_library", - "chromap/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam", - "chromap/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam.bai", - "chromap/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam", - "chromap/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam.bai", - "chromap/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam", - "chromap/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam.bai", - "chromap/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam", - "chromap/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam.bai", - "chromap/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam", - 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"multiqc_nsc_coefficient.yaml:md5,03475a6631170b334d04705afea4576c", - "multiqc_peak_annotation.yaml:md5,4879c78fdd66d6b9518e6462670bab31", - "multiqc_peak_count.yaml:md5,18009097a9da6426b84e23b184bdc46c", - "multiqc_phantompeakqualtools.yaml:md5,6962682a9111dde60ebaaf0fccc27829", - "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,33824d5f5fe73b1c26a872d321708c0a", - "multiqc_picard-1_insertSize.yaml:md5,957775d435d56f52379e24d6b04a2c8e", - "multiqc_picard-1_quality_by_cycle.yaml:md5,11d2fd45c7db4759c8f0743ef1dd9df7", - "multiqc_picard-1_quality_score_distribution.yaml:md5,b14809d683b8b39fad1fe990de1c989e", - "multiqc_picard_baseContent.yaml:md5,544c5cbdfe01bab45549cec414967114", - "multiqc_picard_dups.yaml:md5,87a02182a377c4d4b4160aa71330c29e", - "multiqc_rsc_coefficient.yaml:md5,2d96c8135be53a4a5e425776d2e99702", - "multiqc_samtools_flagstat.yaml:md5,0c6b02ed035229e92036013c88ebce4f", - "multiqc_samtools_flagstat_1.yaml:md5,8b31a5e88418459fa84853ad3f771f77", - "multiqc_samtools_flagstat_2.yaml:md5,fb211e05b13842a922d259a610379065", - "multiqc_samtools_idxstats.yaml:md5,6a409806f4246c0397b29b0142fd8894", - "multiqc_samtools_idxstats_1.yaml:md5,9e825d815fe4642da3a086292dec7792", - "multiqc_samtools_idxstats_2.yaml:md5,7568aab6c7d1b403cff8f07ef503b9cd", - "multiqc_samtools_stats.yaml:md5,9d9b24aceea1c649a84fa5bcb35fa6c6", - "multiqc_samtools_stats_1.yaml:md5,0e4875a9c9c2bfd78588a3ce04ef5caf", - "multiqc_samtools_stats_2.yaml:md5,383b58724b6e90ca35f568ebf6ee8919", - "multiqc_strand_shift_correlation.yaml:md5,14fa8c729c885eea869abeb465ddc31c", - "picard-1_alignment_readlength_plot.yaml:md5,1f645e3a75839bf834fa250fb0e46d91", - "picard-1_alignment_summary_Aligned_Bases.yaml:md5,392fec9f38be3feea5b930209544b972", - "picard-1_alignment_summary_Aligned_Reads.yaml:md5,0c165b0cfff600a509e976c106263b2f", + "multiqc_citations.yaml:md5,c4cdebc20cfc52eb2eee741a36323b3e", + "multiqc_cutadapt.yaml:md5,74b42e87a78ac23b716acec17b3f97b6", + "multiqc_fastqc.yaml:md5,33eb21cad7eafc05b0646954fdeb3e99", + "multiqc_fastqc_1.yaml:md5,7cd54ec9c1c4f5974bd7c3289971a9d5", + "multiqc_nsc_coefficient.yaml:md5,5090cf957c8934ee8b3ef22a8e5186e0", + "multiqc_phantompeakqualtools.yaml:md5,3b2cd02ae6f60d720a6430843f7214e0", + "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,5dd03fb2de4bc031ef4f38506fdf79bd", + "multiqc_picard-1_insertSize.yaml:md5,28c40714dab5d60f553008e41e322bd6", + "multiqc_picard-1_quality_by_cycle.yaml:md5,55a6d144ddafb833e8084c0a73256ea5", + "multiqc_picard-1_quality_score_distribution.yaml:md5,70c20fdc7b8aea86eaf3808885190570", + "multiqc_picard_baseContent.yaml:md5,da52ef94638567b5a8702462ffb673fa", + "multiqc_picard_dups.yaml:md5,55608df298751fbb2eb2cff6e09ca1be", + "multiqc_rsc_coefficient.yaml:md5,07eb8f0961a6df39900dfe74eba40efc", + "multiqc_samtools_flagstat.yaml:md5,20c17552f53ba9a9c484285131588939", + "multiqc_samtools_flagstat_1.yaml:md5,eb06d6348c41d6d328460db1e30b08c2", + "multiqc_samtools_flagstat_2.yaml:md5,d8413a11d98d6b6091c6078ab8b37f57", + "multiqc_samtools_idxstats.yaml:md5,248e9bb33b1e6c932e8d9727054bf479", + "multiqc_samtools_idxstats_1.yaml:md5,248e9bb33b1e6c932e8d9727054bf479", + "multiqc_samtools_idxstats_2.yaml:md5,c28d5216f2f66aa3463a3cc2e9f65e42", + "multiqc_samtools_stats.yaml:md5,389a64168db529d01927f63aa88f0429", + "multiqc_samtools_stats_1.yaml:md5,f938acec2b1ca60b173e0eae74b6fc13", + "multiqc_samtools_stats_2.yaml:md5,cc8e0bd8888efad688a9a6f0a2951c77", + "multiqc_strand_shift_correlation.yaml:md5,1c6e328015484b560c8767f19e2022ac", + "picard-1_alignment_readlength_plot.yaml:md5,afffa0a1961eeecc46cec4c496611771", + "picard-1_alignment_summary_Aligned_Bases.yaml:md5,df552d0592f5f1eca45ae29710b8d124", + "picard-1_alignment_summary_Aligned_Reads.yaml:md5,697e557eeb14941bf1d8dfc4cada7736", "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", - "picard-1_histogram_1.yaml:md5,11d2fd45c7db4759c8f0743ef1dd9df7", - "picard-1_histogram_2.yaml:md5,b14809d683b8b39fad1fe990de1c989e", - "picard-1_insert_size_Counts.yaml:md5,e1f0357f70401d205d452582b84a56d8", - "picard-1_insert_size_Percentages.yaml:md5,ad986dace70bab10123558b1ad6ca619", - "picard-1_quality_by_cycle.yaml:md5,9e7eb35b07281a2aa470445d649346cb", - "picard-1_quality_score_distribution.yaml:md5,84815b05788dcb45af6b2287a563eef7", - "picard_base_distribution_by_cycle__Adenine.yaml:md5,cebb58e48fc182ff663525262d34ff47", - "picard_base_distribution_by_cycle__Cytosine.yaml:md5,546ac75e67fc4be0edca45b4f12fe264", - "picard_base_distribution_by_cycle__Guanine.yaml:md5,76b61f99de3499b422b4310ae567a5c5", - "picard_base_distribution_by_cycle__Thymine.yaml:md5,a4620ac796d26437235bcb4edc3f638d", - "picard_base_distribution_by_cycle__Undetermined.yaml:md5,6984ec68df34f03fec07d6e8d4fec1b2", - "picard_deduplication.yaml:md5,1af3b920ddf0b94d2c617d2ef74e58f1", + "picard-1_histogram_1.yaml:md5,55a6d144ddafb833e8084c0a73256ea5", + "picard-1_histogram_2.yaml:md5,70c20fdc7b8aea86eaf3808885190570", + "picard-1_insert_size_Counts.yaml:md5,8b6774fe6e9f5e90400b32a2cd4e059e", + "picard-1_insert_size_Percentages.yaml:md5,1311fde516d58de45c47466bef63c11f", + "picard-1_quality_by_cycle.yaml:md5,a44bb007bef9a82c91733f281e1641ad", + "picard-1_quality_score_distribution.yaml:md5,7edf8b8c860165ebdbb0118d12a289ef", + "picard_base_distribution_by_cycle__Adenine.yaml:md5,863488d23a0301602bf48a071d97ef94", + "picard_base_distribution_by_cycle__Cytosine.yaml:md5,9bbe42b4d2b57641792aedbffdeebe27", + "picard_base_distribution_by_cycle__Guanine.yaml:md5,ed0a9cf401df8f7e3a3e6a76e7d22fd1", + "picard_base_distribution_by_cycle__Thymine.yaml:md5,2501dc7994af55e76165931bd5af9897", + "picard_base_distribution_by_cycle__Undetermined.yaml:md5,23e62b9c24327183570dbfc3e5b8d61a", + "picard_deduplication.yaml:md5,ed1e94e8b821c9581b62ee151deb057f", "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11", "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11", - "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,c4c251d723c0eb8f771394be7c05b936", - "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,1b1eec5d19ddf1b345b133f2fda62036", - "samtools-flagstat-dp_Percentage_of_total.yaml:md5,da48ca14276999ee304433554ec71838", - "samtools-flagstat-dp_Read_counts-1.yaml:md5,cc68af7fd21bcf37b541c694d581f0e8", - "samtools-flagstat-dp_Read_counts-2.yaml:md5,f9d6bc85d9d764e4ad0b263ffd44b78f", - "samtools-flagstat-dp_Read_counts.yaml:md5,ace0d7287774382756c835fc5b1eedfc", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,2be56aade977cc181057e04a844549bc", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,4a81590c28ff69908533f1531f21d9e2", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,0df5d134d0f597db2ff42153373569a4", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,92a125f968d6c8d527db4a1dfc3ef2b6", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,73158eb30b7790f63c1bd090cd1c9d70", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,d359fb0516c6106fb1a07e6d40d6f260", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,69d094f1c604439690bb0e345fecb580", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,e568afd5cc3a8df573ba648f5b2e42ab", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,a9b9091af444359e66dfc749c8c23453", - "samtools-stats-dp.yaml:md5,dcae905df4f97d6989e53e07acf1b67e", - "samtools_alignment_plot.yaml:md5,b2ec92e142361d39483852b5df683cf6", - "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" + "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,f701f6bc6929098c23dd301beda935f1", + "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,9ae734b04e6bb7ff00baec120d02f4c4", + "samtools-flagstat-dp_Percentage_of_total.yaml:md5,9ae734b04e6bb7ff00baec120d02f4c4", + "samtools-flagstat-dp_Read_counts-1.yaml:md5,d75397929f725917e6314701e564d6a5", + "samtools-flagstat-dp_Read_counts-2.yaml:md5,8f69de6d29829a2153e9b84ac458b8c7", + "samtools-flagstat-dp_Read_counts.yaml:md5,9db7e534c7b7566eeaf7efa2c7337abc", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,0ee5c111e16250fdb8db8255c031f953", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,798ed6bab082ad9309720b3adc8292ad", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,0ee5c111e16250fdb8db8255c031f953", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,2db86aefe33629842f96647fb5785e20", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,33a57019ccb6f1296876439e1383f164", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,2db86aefe33629842f96647fb5785e20", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,75e40606a29c687d9a6e0d7acd891e5b", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,0ae0fa6b698becdd70a9f77977dd5392", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,75e40606a29c687d9a6e0d7acd891e5b", + "samtools-stats-dp.yaml:md5,8155bf8909cdd5b2b15c50837c1734ad", + "samtools_alignment_plot.yaml:md5,0a7e3f5ac8524aaa0a1efd5753372768" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-17T13:22:19.456795982" + "timestamp": "2025-09-18T16:03:14.465547" }, "chromap with stub": { "content": [ - 20 + 19 ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-04T20:51:25.375669" + "timestamp": "2025-09-18T16:03:44.49582" } -} +} \ No newline at end of file diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap index 25abda32d..dfedae657 100644 --- a/tests/skip_consensus_peaks.nf.test.snap +++ b/tests/skip_consensus_peaks.nf.test.snap @@ -1,17 +1,17 @@ { "skip_consensus_peaks with stub": { "content": [ - 20 + 19 ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-04T21:50:26.130655" + "timestamp": "2025-09-18T16:21:59.818685" }, "skip_consensus_peaks": { "content": [ - 210, + 187, { "BAMTOOLS_FILTER": { "bamtools": "2.5.2", @@ -36,9 +36,6 @@ "DEEPTOOLS_COMPUTEMATRIX": { "deeptools": "3.5.5" }, - "DEEPTOOLS_PLOTFINGERPRINT": { - "deeptools": "3.5.5" - }, "DEEPTOOLS_PLOTHEATMAP": { "deeptools": "3.5.5" }, @@ -48,28 +45,15 @@ "FASTQC": { "fastqc": "0.12.1" }, - "FRIP_SCORE": { - "bedtools": "2.30.0", - "samtools": "1.15.1" - }, "GENOME_BLACKLIST_REGIONS": { "bedtools": "2.30.0" }, "GTF2BED": { "perl": "5.26.2" }, - "HOMER_ANNOTATEPEAKS": { - "homer": 4.11 - }, "IGV": { "python": "3.8.3" }, - "MACS3_CALLPEAK": { - "macs3": "3.0.1" - }, - "MULTIQC_CUSTOM_PEAKS": { - "sed": 4.7 - }, "PHANTOMPEAKQUALTOOLS": { "phantompeakqualtools": "1.2.2" }, @@ -82,15 +66,6 @@ "PICARD_MERGESAMFILES": { "picard": "3.2.0-1-g3948afb6b" }, - "PLOT_HOMER_ANNOTATEPEAKS": { - "r-base": "4.0.3" - }, - "PLOT_MACS3_QC": { - "r-base": "4.0.3" - }, - "SAMPLESHEET_CHECK": { - "python": "3.8.3" - }, "SAMTOOLS_FLAGSTAT": { "samtools": "1.22.1" }, @@ -120,258 +95,213 @@ [ "bwa", "bwa/merged_library", - "bwa/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_INPUT_rep1.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_INPUT_rep1.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_INPUT_rep2.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_INPUT_rep2.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T0_rep1.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T0_rep1.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T0_rep2.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T0_rep2.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T15_rep1.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T15_rep1.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T15_rep2.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T15_rep2.mLb.clN.sorted.bam.bai", "bwa/merged_library/bigwig", - "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph", - 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"picard_deduplication.yaml:md5,23d414b202d09aa1234a65f8957c9a9f", "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11", "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11", - "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,823114a992da2bab04eb4edd903746d8", - "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,a97c37a9d95494fe0d02d6e16e6057a6", - "samtools-flagstat-dp_Percentage_of_total.yaml:md5,9c2b32dc86d09eeb870c8fb63d46f9e5", - "samtools-flagstat-dp_Read_counts-1.yaml:md5,d5dfeebe9bff8dd3fcdfdbf32adb106b", - "samtools-flagstat-dp_Read_counts-2.yaml:md5,c3cbc20287333e65b0053c0c644d81f3", - "samtools-flagstat-dp_Read_counts.yaml:md5,265762d51681a3cc1ad8aeb85c71a4e0", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,8837b9900307d0e626f08864e5bdf2cd", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,969627a72da77f241fcca5c19547f6cb", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,55e93fb7b4a86e11fbc2cc0381f4cec3", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,1b97bc9b6f2d353285aa0f873a433754", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,be4649e0e75abcf2d3f8b7cdfce34506", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,63ed0a2b79eb80512305f288c837054d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,ec7d25c50ae159832a8ce0cb8630a03d", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,12259c95d8a4038e99ccdaf583695592", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,5e3a88d956ac7dcc1b7a6d5ae3f3b814", - "samtools-stats-dp.yaml:md5,25a63e73197b0fb5a9c3663698b08589", - "samtools_alignment_plot.yaml:md5,f05cae90c4fb4ff66c4e92eaabd2caf2", - "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" + "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,16b59df2db03579f4ae95a77c0fbec40", + "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,bf6fb2afd80dd224ab92defe404ccca2", + "samtools-flagstat-dp_Percentage_of_total.yaml:md5,95239b971249bf6264a4b22ff28c3fc4", + "samtools-flagstat-dp_Read_counts-1.yaml:md5,19e56322f069010ec5444a1d2e8d8bd2", + "samtools-flagstat-dp_Read_counts-2.yaml:md5,d8861464c2101aaf2664b473cf8f963f", + "samtools-flagstat-dp_Read_counts.yaml:md5,3e2975587543c6257b24a2c0f66a1a41", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,758f206894ae635b8f29248156240502", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,e4c593d018d72665e28a333c389cee40", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,758f206894ae635b8f29248156240502", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,fbf160c68b157724d1dba726849140f4", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,62832c7a2abc4edbe7c1343c54565940", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,fbf160c68b157724d1dba726849140f4", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,c2a4e0b1b50237ec96f01ce158c7b8ab", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,001af4e07c430d2adb71c940a144a81d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,c2a4e0b1b50237ec96f01ce158c7b8ab", + "samtools-stats-dp.yaml:md5,853ab5f91e39616cb6c691091dfdf9d2", + "samtools_alignment_plot.yaml:md5,ec3178a9dce8fdbd383c5045b03b5a59" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-17T11:32:05.17980739" + "timestamp": "2025-09-18T16:21:33.429248" } -} +} \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index b7704fdcf..c0529aee1 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1,11 +1,8 @@ { "skip_trimming": { "content": [ - 209, + 181, { - "ANNOTATE_BOOLEAN_PEAKS": { - "sed": 4.7 - }, "BAMTOOLS_FILTER": { "bamtools": "2.5.2", "samtools": "1.15.1" @@ -29,48 +26,24 @@ "DEEPTOOLS_COMPUTEMATRIX": { "deeptools": "3.5.5" }, - "DEEPTOOLS_PLOTFINGERPRINT": { - "deeptools": "3.5.5" - }, "DEEPTOOLS_PLOTHEATMAP": { "deeptools": "3.5.5" }, "DEEPTOOLS_PLOTPROFILE": { "deeptools": "3.5.5" }, - "DESEQ2_QC": { - "bioconductor-deseq2": "1.28.0", - "r-base": "4.0.3" - }, "FASTQC": { "fastqc": "0.12.1" }, - "FRIP_SCORE": { - "bedtools": "2.30.0", - "samtools": "1.15.1" - }, "GENOME_BLACKLIST_REGIONS": { "bedtools": "2.30.0" }, "GTF2BED": { "perl": "5.26.2" }, - "HOMER_ANNOTATEPEAKS": { - "homer": 4.11 - }, "IGV": { "python": "3.8.3" }, - "MACS3_CALLPEAK": { - "macs3": "3.0.1" - }, - "MACS3_CONSENSUS": { - "python": "3.10.0", - "r-base": "4.1.1" - }, - "MULTIQC_CUSTOM_PEAKS": { - "sed": 4.7 - }, "PHANTOMPEAKQUALTOOLS": { "phantompeakqualtools": "1.2.2" }, @@ -83,15 +56,6 @@ "PICARD_MERGESAMFILES": { "picard": "3.2.0-1-g3948afb6b" }, - "PLOT_HOMER_ANNOTATEPEAKS": { - "r-base": "4.0.3" - }, - "PLOT_MACS3_QC": { - "r-base": "4.0.3" - }, - "SAMPLESHEET_CHECK": { - "python": "3.8.3" - }, "SAMTOOLS_FLAGSTAT": { "samtools": "1.22.1" }, @@ -107,9 +71,6 @@ "SAMTOOLS_STATS": { "samtools": 1.2 }, - "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" - }, "UCSC_BEDGRAPHTOBIGWIG": { "ucsc": 445 }, @@ -120,285 +81,213 @@ [ "bwa", "bwa/merged_library", - "bwa/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam", - "bwa/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam.bai", - "bwa/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam", - 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"multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", @@ -566,9 +435,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", - "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_per_base_n_content_plot.png", @@ -580,16 +446,8 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", - "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", @@ -638,9 +496,6 @@ "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", - "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", @@ -652,16 +507,8 @@ 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"SPT5_T15_REP1.mLb.clN.sorted.bam.stats:md5,2050bd328423c9ef255fd2a56d2e9607", - "SPT5_T15_REP2.mLb.clN.sorted.bam.flagstat:md5,7b3d69e31aac6914877369682086b0ea", - "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,e880a1de98270eb312384d43da1b0595", - "SPT5_T15_REP2.mLb.clN.sorted.bam.stats:md5,041fa26a893e035030e31f792eac5752" + "SPT5_INPUT_rep1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "SPT5_T0_rep1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "SPT5_T15_rep1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-17T13:50:40.996684387" + "timestamp": "2025-09-18T13:22:04.217269" }, "star with stub": { "content": [ - 20 + 18 ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-04T22:40:58.444452" + "timestamp": "2025-09-18T13:22:29.737589" } -} +} \ No newline at end of file diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf index 9817b8e61..f0d0b0d83 100644 --- a/workflows/chipseq.nf +++ b/workflows/chipseq.nf @@ -18,7 +18,7 @@ include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_chipseq_pipeline' -include { INPUT_CHECK } from '../subworkflows/local/input_check' +include { INPUT_CHECK } from '../subworkflows/local/utils_nfcore_chipseq_pipeline' include { ALIGN_STAR } from '../subworkflows/local/align_star' include { BAM_FILTER_BAMTOOLS } from '../subworkflows/local/bam_filter_bamtools' include { BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC } from '../subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc' @@ -234,12 +234,16 @@ workflow CHIPSEQ { meta, bam -> def meta_clone = meta.clone() meta_clone.remove('read_group') - meta_clone.id = meta_clone.id - ~/_T\d+$/ + // Keep samples separate - no merging for this dataset + // Add a unique grouping key to prevent unwanted merging + meta_clone.group_key = meta_clone.id [ meta_clone, bam ] } .groupTuple(by: [0]) .map { meta, bam -> + // Remove the temporary grouping key + meta.remove('group_key') [ meta, bam.flatten() ] } .set { ch_sort_bam }