diff --git a/conf/test.config b/conf/test.config index a06664f..89066ec 100644 --- a/conf/test.config +++ b/conf/test.config @@ -24,8 +24,6 @@ params { max_time = '6.h' outputDir = "test_output" - fastp_path = null - } trace.overwrite = true diff --git a/main.nf b/main.nf index a524d05..3f96759 100644 --- a/main.nf +++ b/main.nf @@ -8,6 +8,7 @@ try { include { createVersionsFile } from './lib/versions.nf' include { format_ngs_agg_opts } from './modules/aggregate_results' include { fastp } from './modules/fastp' +include { mergeFastpJson } from './modules/merge_fastp_json' include { alignReads } from './modules/align_reads' include { mergeAndMarkDuplicates } from './modules/merge_and_mark_duplicates' include { methylDackel_mbias } from './modules/methyldackel_mbias' @@ -83,32 +84,30 @@ workflow { } ///////// Trim, align and mark duplicates ////////// - fastp( passed_bams ) - if (params.single_end) { - fastq_chunks = fastp.out.trimmed_fastq - .flatMap { library, fq_files -> - def fq_list = fq_files instanceof List ? fq_files : [fq_files] - - fq_list.findAll { it.baseName.contains('.1.trimmed.fastq') }.collect { fq1 -> - def chunk_name = fq1.baseName.split(".1.trimmed.fastq")[0] - [library, chunk_name, fq1] - } + // Split each uBAM into byte-range chunks so trimming runs in parallel per chunk. + chunk_size = params.bamslice_chunk_size as long + bam_chunks = passed_bams.flatMap { library, bam -> + def file_size = bam.size() + def chunks = [] + for (long start = 0; start < file_size; start += chunk_size) { + long end = Math.min(start + chunk_size, file_size) + chunks << tuple(library, start, end) } + chunks } - else { - fastq_chunks = fastp.out.trimmed_fastq - .flatMap { library, fq_files -> - def fq_list = fq_files instanceof List ? fq_files : [fq_files] - def chunk_groups = fq_list.groupBy { - it.baseName.replaceAll(/\.[12]\.trimmed\.fastq$/, '') - } - - chunk_groups.collect { chunk_prefix, files -> - def r1 = files.find { it.baseName.contains('.1.trimmed.fastq') } - def r2 = files.find { it.baseName.contains('.2.trimmed.fastq') } - - [library, chunk_prefix, [r1, r2]] - } + + fastp( passed_bams.combine(bam_chunks, by:0) ) + mergeFastpJson( fastp.out.fastp_json.groupTuple() ) + + fastq_chunks = fastp.out.trimmed_fastq.map { library, chunk_name, fq_files -> + def fq_list = fq_files instanceof List ? fq_files : [fq_files] + if (params.single_end) { + tuple(library, chunk_name, fq_list[0]) + } + else { + def r1 = fq_list.find { it.name.contains('.1.trimmed.fastq') } + def r2 = fq_list.find { it.name.contains('.2.trimmed.fastq') } + tuple(library, chunk_name, [r1, r2]) } } alignReads( passed_bams.combine(fastq_chunks, by:0), params.reference_list.bwa_index ) @@ -163,7 +162,7 @@ workflow { ['--bam', mergeAndMarkDuplicates.out.md_bams.map{ tuple(it[0], it[1]) }], ['--bai', mergeAndMarkDuplicates.out.md_bams.map{ tuple(it[0], it[2]) }], ['--metadata_bam_file', bams], - ['--fastp', fastp.out.fastp_json], + ['--fastp', mergeFastpJson.out.merged_json], ['--aln', picard_metrics.out.for_agg ], ['--gc', gc_bias.out.for_agg ], ['--dup', mergeAndMarkDuplicates.out.log], diff --git a/modules/fastp.nf b/modules/fastp.nf index fb38b1f..3d720e0 100644 --- a/modules/fastp.nf +++ b/modules/fastp.nf @@ -1,21 +1,22 @@ process fastp { tag "${library}" label 'low_cpu' - conda "bioconda::samtools=1.21 bioconda::fastp=1.0.1" + conda "bioconda::samtools=1.21 bioconda::fastp=1.3.6 bioconda::bamslice=0.2.1" publishDir "${params.outputDir}/fastp" input: - tuple val(library), path(bam) - + tuple val(library), path(bam), val(start_offset), val(end_offset) + output: - tuple val(library), path("*.trimmed.fastq.gz"), emit: trimmed_fastq - tuple val(library), path("${library}.fastp.json"), emit: fastp_json + tuple val(library), val("${library}_${start_offset}_${end_offset}"), path("${library}_${start_offset}_${end_offset}*.trimmed.fastq.gz"), emit: trimmed_fastq + tuple val(library), val("${library}_${start_offset}_${end_offset}"), path("${library}_${start_offset}_${end_offset}.fastp.json"), emit: fastp_json tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions tuple val("${task.process}"), val('fastp'), eval('fastp --version 2>&1 | cut -f 2 -d " "'), topic: versions - + tuple val("${task.process}"), val('bamslice'), eval('bamslice --version | cut -f 2 -d " "'), topic: versions + script: - def fastp_path = params.fastp_path ? params.fastp_path : '' - def fastp_args = params.single_end ? "--out1 ${library}.1.trimmed.fastq.gz" : "--interleaved_in --out1 ${library}.1.trimmed.fastq.gz --out2 ${library}.2.trimmed.fastq.gz" + def chunk = "${library}_${start_offset}_${end_offset}" + def fastp_args = params.single_end ? "--out1 ${chunk}.1.trimmed.fastq.gz" : "--interleaved_in --out1 ${chunk}.1.trimmed.fastq.gz --out2 ${chunk}.2.trimmed.fastq.gz" """ set +o pipefail inst_name=\$(samtools view ${bam} | head -n 1 | cut -d ":" -f 1) @@ -23,14 +24,13 @@ process fastp { trim_polyg=\$(echo "\${inst_name}" | awk '{if (\$1~/^A0|^NB|^NS|^VH/) {print "--trim_poly_g"} else {print ""}}') echo \${trim_polyg} | awk '{ if (length(\$1)>0) { print "2-color instrument: poly-g trim mode on" } }' - - samtools fastq -n ${bam} | \\ - ${fastp_path}fastp --stdin \\ + + bamslice --input ${bam} --start-offset ${start_offset} --end-offset ${end_offset} | \\ + fastp --stdin \\ -l 2 -Q \${trim_polyg} \\ --thread 1 \\ --overrepresentation_analysis \\ - -j "${library}.fastp.json" \\ - --split_by_lines ${params.fastq_split_lines} \\ + -j "${chunk}.fastp.json" \\ ${fastp_args} """ } diff --git a/modules/merge_fastp_json.nf b/modules/merge_fastp_json.nf new file mode 100644 index 0000000..0b057d1 --- /dev/null +++ b/modules/merge_fastp_json.nf @@ -0,0 +1,18 @@ +process mergeFastpJson { + tag "${library}" + label 'low_cpu' + conda 'bioconda::bamslice=0.2.1' + publishDir "${params.outputDir}/fastp" + + input: + tuple val(library), val(_slices), path(json_files) + + output: + tuple val(library), path("${library}.fastp.json"), emit: merged_json + tuple val("${task.process}"), val('bamslice'), eval('bamslice --version | cut -f 2 -d " "'), topic: versions + + script: + """ + fastp-merge ${json_files.join(' ')} -o ${library}.fastp.json + """ +} diff --git a/nextflow.config b/nextflow.config index b31b4fe..32e77e3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,7 @@ params { workflow = 'EM-seq' outputDir = "em-seq_output" tmp_dir = '/tmp' - fastq_split_lines = 8000000 // approx 4M reads + bamslice_chunk_size = 212121330 // For 2x100 reads, ~4.8M reads enable_neb_agg = false skip_target_bed = false target_bed_slop = 50 diff --git a/tests/main.nf.test b/tests/main.nf.test index 541c807..d3270ef 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -11,14 +11,14 @@ nextflow_pipeline { params.genome = 'test' params.email = 'foo@example.com' params.flowcell = "test_pipeline" - params.fastq_split_lines = 4000 + params.bamslice_chunk_size = 250000 params.enable_neb_agg = true - + } then { - def bwameth_file_1 = bam("${launchDir}/test_output/bwameth_align/0001.emseq-test1.aln.bam").getStatistics() - def bwameth_file_2 = bam("${launchDir}/test_output/bwameth_align/0002.emseq-test1.aln.bam").getStatistics() + def bwameth_file_1 = bam("${launchDir}/test_output/bwameth_align/emseq-test1_0_250000.aln.bam").getStatistics() + def bwameth_file_2 = bam("${launchDir}/test_output/bwameth_align/emseq-test1_250000_421605.aln.bam").getStatistics() def fastqc = path("${launchDir}/test_output/stats/fastqc/emseq-test1.md_fastqc.html").exists() def fastp = path("${launchDir}/test_output/fastp/emseq-test1.fastp.json").text.tokenize('\n')[1..33] def markdup = bam("${launchDir}/test_output/markduped_bams/emseq-test1.md.bam").getStatistics() @@ -30,7 +30,7 @@ nextflow_pipeline { def alignment_metrics = path("${launchDir}/test_output/stats/picard_alignment_metrics/emseq-test1.alignment_summary_metrics.txt").text.tokenize('\n')[5..8] def methyldackel_extract = path("${launchDir}/test_output/methylDackelExtracts/emseq-test1_CpG.methylKit.gz").md5 def mbias = path("${launchDir}/test_output/methylDackelExtracts/mbias/emseq-test1.combined_mbias.tsv").md5 - def nonconverted = path("${launchDir}/test_output/bwameth_align/0001.emseq-test1.nonconverted_counts.tsv").text.tokenize('\n') + def nonconverted = path("${launchDir}/test_output/bwameth_align/emseq-test1_0_250000.nonconverted_counts.tsv").text.tokenize('\n') def nonconverted_combined = path("${launchDir}/test_output/stats/nonconverted_counts/emseq-test1.nonconverted_counts.for_agg.tsv").text.tokenize('\n') def combined_summaries = path("${launchDir}/test_output/methylKit_intersections/positional_summaries_combined.tsv").exists() def positional_summary = path("${launchDir}/test_output/methylKit_intersections/emseq-test1_vs_emseq_test_regions_positional_summary.tsv").text.tokenize('\n') @@ -77,15 +77,15 @@ nextflow_pipeline { params.genome = 'test' params.email = 'foo@example.com' params.flowcell = "test_pipeline" - params.fastq_split_lines = 4000 + params.bamslice_chunk_size = 250000 params.enable_neb_agg = true params.single_end = true - + } then { - def bwameth_file_1 = bam("${launchDir}/test_output/bwameth_align/0001.emseq-test1.aln.bam").getStatistics() - def bwameth_file_2 = bam("${launchDir}/test_output/bwameth_align/0002.emseq-test1.aln.bam").getStatistics() + def bwameth_file_1 = bam("${launchDir}/test_output/bwameth_align/emseq-test1_0_250000.aln.bam").getStatistics() + def bwameth_file_2 = bam("${launchDir}/test_output/bwameth_align/emseq-test1_250000_421605.aln.bam").getStatistics() def fastqc = path("${launchDir}/test_output/stats/fastqc/emseq-test1.md_fastqc.html").exists() def fastp = path("${launchDir}/test_output/fastp/emseq-test1.fastp.json").text.tokenize('\n')[1..33] def markdup = bam("${launchDir}/test_output/markduped_bams/emseq-test1.md.bam").getStatistics() @@ -96,7 +96,7 @@ nextflow_pipeline { def alignment_metrics = path("${launchDir}/test_output/stats/picard_alignment_metrics/emseq-test1.alignment_summary_metrics.txt").text.tokenize('\n')[5..8] def methyldackel_extract = path("${launchDir}/test_output/methylDackelExtracts/emseq-test1_CpG.methylKit.gz").md5 def mbias = path("${launchDir}/test_output/methylDackelExtracts/mbias/emseq-test1.combined_mbias.tsv").md5 - def nonconverted = path("${launchDir}/test_output/bwameth_align/0001.emseq-test1.nonconverted_counts.tsv").text.tokenize('\n') + def nonconverted = path("${launchDir}/test_output/bwameth_align/emseq-test1_0_250000.nonconverted_counts.tsv").text.tokenize('\n') def nonconverted_combined = path("${launchDir}/test_output/stats/nonconverted_counts/emseq-test1.nonconverted_counts.for_agg.tsv").text.tokenize('\n') def combined_summaries = path("${launchDir}/test_output/methylKit_intersections/positional_summaries_combined.tsv").exists() def positional_summary = path("${launchDir}/test_output/methylKit_intersections/emseq-test1_vs_emseq_test_regions_positional_summary.tsv").text.tokenize('\n') diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index d757b75..08ffd9a 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -3,19 +3,19 @@ "content": [ { "tasksFailed": 0, - "tasksCount": 59, - "tasksSucceeded": 59 + "tasksCount": 47, + "tasksSucceeded": 47 }, [ "bwameth_file_1", { "maxReadLength": 76, - "minReadLength": 41, + "minReadLength": 44, "meanReadLength": 75, "maxQuality": 60, "minQuality": 0, - "meanQuality": 9, - "readCount": 150 + "meanQuality": 10, + "readCount": 705 } ], [ @@ -26,8 +26,8 @@ "meanReadLength": 76, "maxQuality": 60, "minQuality": 0, - "meanQuality": 20, - "readCount": 75 + "meanQuality": 8, + "readCount": 399 } ], [ @@ -38,77 +38,77 @@ "fastp", [ "\t\"summary\": {", - "\t\t\"fastp_version\": \"1.0.1\",", + "\t\t\"fastp_version\": \"1.3.6\",", "\t\t\"sequencing\": \"single end (76 cycles)\",", "\t\t\"before_filtering\": {", - "\t\t\t\"total_reads\":9534,", - "\t\t\t\"total_bases\":724584,", - "\t\t\t\"q20_bases\":681052,", - "\t\t\t\"q30_bases\":662196,", - "\t\t\t\"q20_rate\":0.939921,", - "\t\t\t\"q30_rate\":0.913898,", - "\t\t\t\"read1_mean_length\":76,", - "\t\t\t\"gc_content\":0.218668", + "\t\t\t\"total_reads\": 9534,", + "\t\t\t\"total_bases\": 724584,", + "\t\t\t\"q20_bases\": 681052,", + "\t\t\t\"q30_bases\": 662196,", + "\t\t\t\"q20_rate\": 0.939921,", + "\t\t\t\"q30_rate\": 0.913898,", + "\t\t\t\"read1_mean_length\": 76,", + "\t\t\t\"gc_content\": 0.218667", "\t\t},", "\t\t\"after_filtering\": {", - "\t\t\t\"total_reads\":9530,", - "\t\t\t\"total_bases\":724053,", - "\t\t\t\"q20_bases\":680589,", - "\t\t\t\"q30_bases\":661741,", - "\t\t\t\"q20_rate\":0.939971,", - "\t\t\t\"q30_rate\":0.91394,", - "\t\t\t\"read1_mean_length\":75,", - "\t\t\t\"gc_content\":0.218099", + "\t\t\t\"total_reads\": 9530,", + "\t\t\t\"total_bases\": 724053,", + "\t\t\t\"q20_bases\": 680589,", + "\t\t\t\"q30_bases\": 661741,", + "\t\t\t\"q20_rate\": 0.939971,", + "\t\t\t\"q30_rate\": 0.91394,", + "\t\t\t\"read1_mean_length\": 75,", + "\t\t\t\"gc_content\": 0.218099", "\t\t}", "\t},", "\t\"filtering_result\": {", "\t\t\"passed_filter_reads\": 9530,", "\t\t\"low_quality_reads\": 0,", "\t\t\"too_many_N_reads\": 0,", + "\t\t\"adapter_dimer_reads\": 0,", "\t\t\"too_short_reads\": 4,", "\t\t\"too_long_reads\": 0", "\t},", - "\t\"duplication\": {", - "\t\t\"rate\": 0.00125865" + "\t\"duplication\": {" ] ], [ "markdup", { "maxReadLength": 76, - "minReadLength": 41, + "minReadLength": 44, "meanReadLength": 75, "maxQuality": 60, "minQuality": 0, - "meanQuality": 16, - "readCount": 808 + "meanQuality": 9, + "readCount": 1104 } ], [ "markdup_log", [ "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tSECONDARY_OR_SUPPLEMENTARY_RDS\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE", - "Oct25_PV_10ngR3_F6\t806\t0\t2\t0\t50\t0\t0\t0.062035\t" + "Oct25_PV_10ngR3_F6\t1103\t0\t1\t0\t81\t0\t0\t0.073436\t" ] ], [ "idxstats", [ - "chr1\t284940\t808\t0", + "chr1\t284940\t1104\t0", "*\t0\t0\t0" ] ], [ "flagstats", [ - "798 + 10 in total (QC-passed reads + QC-failed reads)", - "796 + 10 primary", - "2 + 0 secondary", + "1098 + 6 in total (QC-passed reads + QC-failed reads)", + "1097 + 6 primary", + "1 + 0 secondary", "0 + 0 supplementary", - "49 + 1 duplicates", - "49 + 1 primary duplicates", - "798 + 10 mapped (100.00% : 100.00%)", - "796 + 10 primary mapped (100.00% : 100.00%)", + "81 + 0 duplicates", + "81 + 0 primary duplicates", + "1098 + 6 mapped (100.00% : 100.00%)", + "1097 + 6 primary mapped (100.00% : 100.00%)", "0 + 0 paired in sequencing", "0 + 0 read1", "0 + 0 read2", @@ -123,59 +123,59 @@ "gc_bias", [ "ACCUMULATION_LEVEL\tREADS_USED\tGC\tWINDOWS\tREAD_STARTS\tMEAN_BASE_QUALITY\tNORMALIZED_COVERAGE\tERROR_BAR_WIDTH\tSAMPLE\tLIBRARY\tREAD_GROUP", - "All Reads\tALL\t0\t17252\t29\t6\t0.59258\t0.110039\t\t\t", - "All Reads\tALL\t1\t3503\t15\t7\t1.509521\t0.389757\t\t\t", - "All Reads\tALL\t2\t5640\t17\t7\t1.062571\t0.257711\t\t\t", - "All Reads\tALL\t3\t3475\t10\t7\t1.014456\t0.320799\t\t\t", - "All Reads\tALL\t4\t4275\t8\t6\t0.659693\t0.233237\t\t\t", - "All Reads\tALL\t5\t3480\t6\t7\t0.607799\t0.248133\t\t\t", - "All Reads\tALL\t6\t3400\t5\t7\t0.518417\t0.231843\t\t\t", - "All Reads\tALL\t7\t3235\t9\t6\t0.980745\t0.326915\t\t\t", - "All Reads\tALL\t8\t3640\t9\t8\t0.871624\t0.290541\t\t\t", - "All Reads\tALL\t9\t3412\t8\t8\t0.82655\t0.29223\t\t\t", - "All Reads\tALL\t10\t3608\t6\t7\t0.586236\t0.23933\t\t\t", - "All Reads\tALL\t11\t3699\t6\t7\t0.571814\t0.233442\t\t\t", - "All Reads\tALL\t12\t3840\t4\t10\t0.367212\t0.183606\t\t\t", - "All Reads\tALL\t13\t3874\t13\t9\t1.182965\t0.328095\t\t\t", - "All Reads\tALL\t14\t3693\t9\t9\t0.859115\t0.286372\t\t\t", - "All Reads\tALL\t15\t3986\t19\t9\t1.680368\t0.385503\t\t\t", - "All Reads\tALL\t16\t3911\t19\t10\t1.712592\t0.392896\t\t\t", - "All Reads\tALL\t17\t3778\t22\t9\t2.05281\t0.437661\t\t\t", - "All Reads\tALL\t18\t3793\t22\t9\t2.044692\t0.43593\t\t\t", - "All Reads\tALL\t19\t3698\t26\t9\t2.478532\t0.48608\t\t\t", - "All Reads\tALL\t20\t3735\t27\t9\t2.548363\t0.490433\t\t\t", - "All Reads\tALL\t21\t3759\t30\t8\t2.813436\t0.513661\t\t\t", - "All Reads\tALL\t22\t3461\t34\t9\t3.463103\t0.593917\t\t\t", - "All Reads\tALL\t23\t3475\t32\t10\t3.24626\t0.573863\t\t\t", - "All Reads\tALL\t24\t3393\t48\t9\t4.98707\t0.719822\t\t\t", - "All Reads\tALL\t25\t3365\t48\t8\t5.028567\t0.725811\t\t\t", - "All Reads\tALL\t26\t3200\t41\t9\t4.516708\t0.705391\t\t\t", - "All Reads\tALL\t27\t2988\t45\t10\t5.309089\t0.791432\t\t\t", - "All Reads\tALL\t28\t2852\t33\t10\t4.078989\t0.710061\t\t\t", - "All Reads\tALL\t29\t2805\t27\t9\t3.393274\t0.653036\t\t\t", - "All Reads\tALL\t30\t2833\t12\t8\t1.493216\t0.431054\t\t\t", - "All Reads\tALL\t31\t2731\t26\t9\t3.356137\t0.658193\t\t\t", - "All Reads\tALL\t32\t2760\t31\t9\t3.959503\t0.711148\t\t\t", - "All Reads\tALL\t33\t2776\t18\t9\t2.285815\t0.538772\t\t\t", - "All Reads\tALL\t34\t2475\t13\t10\t1.851639\t0.513552\t\t\t", - "All Reads\tALL\t35\t2672\t11\t7\t1.451257\t0.43757\t\t\t", - "All Reads\tALL\t36\t2796\t7\t10\t0.88257\t0.33358\t\t\t", - "All Reads\tALL\t37\t2850\t9\t12\t1.113232\t0.371077\t\t\t", - "All Reads\tALL\t38\t2826\t10\t10\t1.247429\t0.394472\t\t\t", - "All Reads\tALL\t39\t3054\t5\t10\t0.57715\t0.25811\t\t\t", - "All Reads\tALL\t40\t3449\t6\t10\t0.613262\t0.250363\t\t\t", - "All Reads\tALL\t41\t4012\t8\t6\t0.702938\t0.248526\t\t\t", - "All Reads\tALL\t42\t4971\t10\t7\t0.70916\t0.224256\t\t\t", - "All Reads\tALL\t43\t5630\t2\t7\t0.12523\t0.088551\t\t\t", - "All Reads\tALL\t44\t6409\t2\t11\t0.110009\t0.077788\t\t\t", - "All Reads\tALL\t45\t7297\t3\t9\t0.144932\t0.083677\t\t\t", - "All Reads\tALL\t46\t8146\t3\t11\t0.129827\t0.074956\t\t\t", - "All Reads\tALL\t47\t8876\t1\t8\t0.039716\t0.039716\t\t\t", - "All Reads\tALL\t48\t9213\t0\t0\t0\t0\t\t\t", - "All Reads\tALL\t49\t9815\t1\t2\t0.035917\t0.035917\t\t\t", - "All Reads\tALL\t50\t10134\t2\t4\t0.069572\t0.049195\t\t\t", - "All Reads\tALL\t51\t9913\t1\t16\t0.035562\t0.035562\t\t\t", - "All Reads\tALL\t52\t9189\t0\t0\t0\t0\t\t\t", + "All Reads\tALL\t0\t17252\t122\t6\t1.824529\t0.165185\t\t\t", + "All Reads\tALL\t1\t3503\t37\t6\t2.72516\t0.448014\t\t\t", + "All Reads\tALL\t2\t5640\t47\t6\t2.150053\t0.313617\t\t\t", + "All Reads\tALL\t3\t3475\t40\t6\t2.969857\t0.469576\t\t\t", + "All Reads\tALL\t4\t4275\t45\t6\t2.715856\t0.404856\t\t\t", + "All Reads\tALL\t5\t3480\t18\t5\t1.334516\t0.314548\t\t\t", + "All Reads\tALL\t6\t3400\t23\t5\t1.745337\t0.363928\t\t\t", + "All Reads\tALL\t7\t3235\t19\t6\t1.515339\t0.347643\t\t\t", + "All Reads\tALL\t8\t3640\t7\t6\t0.496166\t0.187533\t\t\t", + "All Reads\tALL\t9\t3412\t11\t6\t0.831791\t0.250794\t\t\t", + "All Reads\tALL\t10\t3608\t13\t6\t0.929624\t0.257831\t\t\t", + "All Reads\tALL\t11\t3699\t12\t6\t0.837004\t0.241622\t\t\t", + "All Reads\tALL\t12\t3840\t7\t6\t0.470324\t0.177766\t\t\t", + "All Reads\tALL\t13\t3874\t8\t7\t0.532796\t0.188372\t\t\t", + "All Reads\tALL\t14\t3693\t15\t6\t1.047954\t0.270581\t\t\t", + "All Reads\tALL\t15\t3986\t22\t7\t1.424019\t0.303602\t\t\t", + "All Reads\tALL\t16\t3911\t17\t7\t1.12148\t0.271999\t\t\t", + "All Reads\tALL\t17\t3778\t16\t7\t1.092668\t0.273167\t\t\t", + "All Reads\tALL\t18\t3793\t25\t8\t1.700543\t0.340109\t\t\t", + "All Reads\tALL\t19\t3698\t30\t7\t2.093075\t0.382141\t\t\t", + "All Reads\tALL\t20\t3735\t28\t7\t1.934184\t0.365526\t\t\t", + "All Reads\tALL\t21\t3759\t34\t6\t2.333657\t0.400219\t\t\t", + "All Reads\tALL\t22\t3461\t34\t6\t2.53459\t0.434679\t\t\t", + "All Reads\tALL\t23\t3475\t41\t7\t3.044104\t0.475409\t\t\t", + "All Reads\tALL\t24\t3393\t62\t7\t4.714528\t0.598746\t\t\t", + "All Reads\tALL\t25\t3365\t52\t7\t3.987022\t0.5529\t\t\t", + "All Reads\tALL\t26\t3200\t43\t6\t3.46696\t0.528706\t\t\t", + "All Reads\tALL\t27\t2988\t38\t8\t3.281205\t0.532282\t\t\t", + "All Reads\tALL\t28\t2852\t35\t6\t3.166277\t0.535198\t\t\t", + "All Reads\tALL\t29\t2805\t29\t8\t2.667445\t0.495332\t\t\t", + "All Reads\tALL\t30\t2833\t10\t5\t0.910718\t0.287994\t\t\t", + "All Reads\tALL\t31\t2731\t24\t6\t2.267357\t0.462822\t\t\t", + "All Reads\tALL\t32\t2760\t25\t8\t2.337014\t0.467403\t\t\t", + "All Reads\tALL\t33\t2776\t16\t6\t1.487068\t0.371767\t\t\t", + "All Reads\tALL\t34\t2475\t15\t5\t1.563675\t0.403739\t\t\t", + "All Reads\tALL\t35\t2672\t14\t6\t1.35183\t0.361292\t\t\t", + "All Reads\tALL\t36\t2796\t7\t8\t0.645939\t0.244142\t\t\t", + "All Reads\tALL\t37\t2850\t9\t12\t0.814757\t0.271586\t\t\t", + "All Reads\tALL\t38\t2826\t11\t7\t1.004271\t0.302799\t\t\t", + "All Reads\tALL\t39\t3054\t4\t10\t0.337926\t0.168963\t\t\t", + "All Reads\tALL\t40\t3449\t7\t8\t0.523643\t0.197918\t\t\t", + "All Reads\tALL\t41\t4012\t9\t5\t0.578778\t0.192926\t\t\t", + "All Reads\tALL\t42\t4971\t7\t5\t0.363316\t0.137321\t\t\t", + "All Reads\tALL\t43\t5630\t5\t6\t0.229135\t0.102472\t\t\t", + "All Reads\tALL\t44\t6409\t2\t11\t0.080514\t0.056932\t\t\t", + "All Reads\tALL\t45\t7297\t2\t8\t0.070716\t0.050004\t\t\t", + "All Reads\tALL\t46\t8146\t2\t10\t0.063346\t0.044792\t\t\t", + "All Reads\tALL\t47\t8876\t1\t8\t0.029068\t0.029068\t\t\t", + "All Reads\tALL\t48\t9213\t1\t11\t0.028005\t0.028005\t\t\t", + "All Reads\tALL\t49\t9815\t0\t0\t0\t0\t\t\t", + "All Reads\tALL\t50\t10134\t1\t6\t0.025459\t0.025459\t\t\t", + "All Reads\tALL\t51\t9913\t1\t3\t0.026027\t0.026027\t\t\t", + "All Reads\tALL\t52\t9189\t1\t2\t0.028078\t0.028078\t\t\t", "All Reads\tALL\t53\t8455\t0\t0\t0\t0\t\t\t", "All Reads\tALL\t54\t7312\t0\t0\t0\t0\t\t\t", "All Reads\tALL\t55\t5984\t0\t0\t0\t0\t\t\t", @@ -230,18 +230,18 @@ "alignment_metrics", [ "CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tSD_READ_LENGTH\tMEDIAN_READ_LENGTH\tMAD_READ_LENGTH\tMIN_READ_LENGTH\tMAX_READ_LENGTH\tMEAN_ALIGNED_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER\tPCT_SOFTCLIP\tPCT_HARDCLIP\tAVG_POS_3PRIME_SOFTCLIP_LENGTH\tSAMPLE\tLIBRARY\tREAD_GROUP", - "UNPAIRED\t806\t796\t0.987593\t0\t796\t1\t58374\t266\t19588\t18487\t0\t0.117934\t0.093539\t0.004094\t75.979899\t0.567105\t76\t0\t60\t76\t73.664573\t0\t0\t0\t0\t0\t0.498744\t0.007519\t0\t0.030473\t0\t17.479167\t\t\t", + "UNPAIRED\t1103\t1097\t0.99456\t0\t1097\t1\t80947\t226\t16700\t15898\t0\t0.205179\t0.161504\t0.00462\t75.985415\t0.483077\t76\t0\t60\t76\t74.128532\t0\t0\t0\t0\t0\t0.673655\t0.004425\t0\t0.024437\t0\t17.966102\t\t\t", "## HISTOGRAM\tjava.lang.Integer", "READ_LENGTH\tUNPAIRED_TOTAL_LENGTH_COUNT\tUNPAIRED_ALIGNED_LENGTH_COUNT" ] ], [ "methyldackel_extract", - "d2515e17f0fa2189b159151f27cc4261" + "01ab9aaf9c0d3a1c65c36f362dda815b" ], [ "mbias", - "fae5d73101b86e036b37f7446847400b" + "9c258a491c66ef4e460aa329fca5e202" ], [ "nonconverted", @@ -259,31 +259,8 @@ "positional_summary", [ "methylkit_file\tchr\ttarget_length\tposition\tcontext\tmean_methylation\tn_loci\tn_measurements", - "emseq-test1\tchr1\t182\t177\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t187\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t199\tCHH\t50\t1\t1", - "emseq-test1\tchr1\t204\t179\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t182\t167\tCHH\t0\t1\t1", - "emseq-test1\tchr1\t204\t194\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t182\t180\tCHG\t100\t1\t1", - "emseq-test1\tchr1\t204\t192\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t190\tCG\t100\t1\t1", - "emseq-test1\tchr1\t204\t182\tCHH\t100\t1\t1", "emseq-test1\tchr1\t182\t178\tCG\t0\t1\t1", - "emseq-test1\tchr1\t182\t170\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t188\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t182\t176\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t182\t179\tCG\t100\t1\t1", - "emseq-test1\tchr1\t182\t174\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t189\tCG\t0\t1\t1", - "emseq-test1\tchr1\t204\t181\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t178\tCHH\t0\t1\t1", - "emseq-test1\tchr1\t204\t191\tCHG\t100\t1\t1", - "emseq-test1\tchr1\t182\t181\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t185\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t182\t171\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t182\t168\tCHH\t100\t1\t1", - "emseq-test1\tchr1\t204\t203\tCHH\t100\t1\t1" + "emseq-test1\tchr1\t204\t189\tCG\t0\t1\t1" ] ], [ @@ -294,43 +271,16 @@ "region_summary", [ "library\ttarget_locus\ttarget_name\tcontext\tmean_methylation", - "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCG\t50", - "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCHG\t100", - "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCHH\t86.36363636", - "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCG\t50", - "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCHG\t100", - "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCHH\t87.5" + "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCG\t0", + "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCG\t0" ] ], [ "methylkit_intersections", [ "methylkit_file\tchr\tstart\tend\tcontext\tmethylation\ttarget_locus\ttarget_name", - "emseq-test2\tchr1\t141016\t141017\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141017\t141018\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141019\t141020\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141020\t141021\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141023\t141024\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141025\t141026\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141026\t141027\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", "emseq-test2\tchr1\t141027\t141028\tCG\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141028\t141029\tCG\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141029\t141030\tCHG\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141030\t141031\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141032\t141033\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141037\t141038\tCHH\t50\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141041\t141042\tCHH\t100\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141016\t141017\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141017\t141018\tCHH\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141019\t141020\tCHH\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141020\t141021\tCHH\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141023\t141024\tCHH\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141025\t141026\tCHH\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141026\t141027\tCHH\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141027\t141028\tCG\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141028\t141029\tCG\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141029\t141030\tCHG\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", - "emseq-test2\tchr1\t141030\t141031\tCHH\t100\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG" + "emseq-test2\tchr1\t141027\t141028\tCG\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG" ] ], [ @@ -364,39 +314,39 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2025-09-17T10:24:44.861870934" + "timestamp": "2026-07-02T13:08:19.546823" }, "EM-seq workflow uBam": { "content": [ { "tasksFailed": 0, - "tasksCount": 51, - "tasksSucceeded": 51 + "tasksCount": 49, + "tasksSucceeded": 49 }, [ "bwameth_file_1", { "maxReadLength": 76, - "minReadLength": 38, + "minReadLength": 32, "meanReadLength": 74, "maxQuality": 60, "minQuality": 0, "meanQuality": 18, - "readCount": 401 + "readCount": 1105 } ], [ "bwameth_file_2", { "maxReadLength": 76, - "minReadLength": 32, - "meanReadLength": 75, + "minReadLength": 31, + "meanReadLength": 74, "maxQuality": 60, "minQuality": 0, - "meanQuality": 18, - "readCount": 370 + "meanQuality": 19, + "readCount": 694 } ], [ @@ -407,64 +357,64 @@ "fastp", [ "\t\"summary\": {", - "\t\t\"fastp_version\": \"1.0.1\",", + "\t\t\"fastp_version\": \"1.3.6\",", "\t\t\"sequencing\": \"paired end (76 cycles + 76 cycles)\",", "\t\t\"before_filtering\": {", - "\t\t\t\"total_reads\":9534,", - "\t\t\t\"total_bases\":724584,", - "\t\t\t\"q20_bases\":681052,", - "\t\t\t\"q30_bases\":662196,", - "\t\t\t\"q20_rate\":0.939921,", - "\t\t\t\"q30_rate\":0.913898,", - "\t\t\t\"read1_mean_length\":76,", - "\t\t\t\"read2_mean_length\":76,", - "\t\t\t\"gc_content\":0.218668", + "\t\t\t\"total_reads\": 9534,", + "\t\t\t\"total_bases\": 724584,", + "\t\t\t\"q20_bases\": 681052,", + "\t\t\t\"q30_bases\": 662196,", + "\t\t\t\"q20_rate\": 0.939921,", + "\t\t\t\"q30_rate\": 0.913898,", + "\t\t\t\"read1_mean_length\": 76,", + "\t\t\t\"read2_mean_length\": 76,", + "\t\t\t\"gc_content\": 0.218667", "\t\t},", "\t\t\"after_filtering\": {", - "\t\t\t\"total_reads\":9526,", - "\t\t\t\"total_bases\":719174,", - "\t\t\t\"q20_bases\":676534,", - "\t\t\t\"q30_bases\":657910,", - "\t\t\t\"q20_rate\":0.94071,", - "\t\t\t\"q30_rate\":0.914813,", - "\t\t\t\"read1_mean_length\":75,", - "\t\t\t\"read2_mean_length\":75,", - "\t\t\t\"gc_content\":0.216799", + "\t\t\t\"total_reads\": 9526,", + "\t\t\t\"total_bases\": 719174,", + "\t\t\t\"q20_bases\": 676534,", + "\t\t\t\"q30_bases\": 657910,", + "\t\t\t\"q20_rate\": 0.94071,", + "\t\t\t\"q30_rate\": 0.914813,", + "\t\t\t\"read1_mean_length\": 75,", + "\t\t\t\"read2_mean_length\": 75,", + "\t\t\t\"gc_content\": 0.216799", "\t\t}", "\t},", "\t\"filtering_result\": {", "\t\t\"passed_filter_reads\": 9526,", "\t\t\"low_quality_reads\": 0,", "\t\t\"too_many_N_reads\": 0,", + "\t\t\"adapter_dimer_reads\": 0,", "\t\t\"too_short_reads\": 8,", - "\t\t\"too_long_reads\": 0", - "\t}," + "\t\t\"too_long_reads\": 0" ] ], [ "markdup", { "maxReadLength": 76, - "minReadLength": 32, - "meanReadLength": 75, + "minReadLength": 31, + "meanReadLength": 74, "maxQuality": 60, "minQuality": 0, - "meanQuality": 14, - "readCount": 1433 + "meanQuality": 18, + "readCount": 1799 } ], [ "markdup_log", [ "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tSECONDARY_OR_SUPPLEMENTARY_RDS\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE", - "Oct25_PV_10ngR3_F6\t368\t348\t1\t368\t35\t0\t0\t0.032895\t" + "Oct25_PV_10ngR3_F6\t264\t635\t1\t264\t24\t0\t0\t0.015645\t" ] ], [ "insert_sizes", [ - "100\t105\t27\t11\t149721\t95.181102\t34.677521\t135\tFR\t11\t17\t29\t39\t55\t71\t87\t101\t131\t46211\t288395\t\t\t", - "92214\t43427\t28743\t43427\t121212\t93665.6\t31778.751255\t5\tRF\t1\t1\t3393\t3393\t57487\t57487\t57997\t57997\t97575\t97575\t97575\t\t\t", + "95\t92\t31.5\t5\t149721\t92.498282\t40.521886\t294\tFR\t11\t23\t41\t49\t63\t77\t89\t109\t133\t161\t143493\t\t\t", + "120957\t43427\t255\t43427\t121212\t95198.666667\t44835.759817\t3\tRF\t1\t1\t1\t511\t511\t511\t155061\t155061\t155061\t155061\t155061\t\t\t", "0\t0\t0\t0\t0\t0\t0\t0\tTANDEM\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\t\t", "## HISTOGRAM\tjava.lang.Integer" ] @@ -472,27 +422,27 @@ [ "idxstats", [ - "chr1\t284940\t1065\t368", + "chr1\t284940\t1535\t264", "*\t0\t0\t0" ] ], [ "flagstats", [ - "1165 + 268 in total (QC-passed reads + QC-failed reads)", - "1164 + 268 primary", + "1215 + 584 in total (QC-passed reads + QC-failed reads)", + "1214 + 584 primary", "1 + 0 secondary", "0 + 0 supplementary", - "33 + 2 duplicates", - "33 + 2 primary duplicates", - "802 + 263 mapped (68.84% : 98.13%)", - "801 + 263 primary mapped (68.81% : 98.13%)", - "1164 + 268 paired in sequencing", - "582 + 134 read1", - "582 + 134 read2", - "272 + 0 properly paired (23.37% : 0.00%)", - "438 + 258 with itself and mate mapped", - "363 + 5 singletons (31.19% : 1.87%)", + "22 + 2 duplicates", + "22 + 2 primary duplicates", + "956 + 579 mapped (78.68% : 99.14%)", + "955 + 579 primary mapped (78.67% : 99.14%)", + "1214 + 584 paired in sequencing", + "607 + 292 read1", + "607 + 292 read2", + "674 + 0 properly paired (55.52% : 0.00%)", + "696 + 574 with itself and mate mapped", + "259 + 5 singletons (21.33% : 0.86%)", "0 + 0 with mate mapped to a different chr", "0 + 0 with mate mapped to a different chr (mapQ>=5)" ] @@ -501,66 +451,66 @@ "gc_bias", [ "ACCUMULATION_LEVEL\tREADS_USED\tGC\tWINDOWS\tREAD_STARTS\tMEAN_BASE_QUALITY\tNORMALIZED_COVERAGE\tERROR_BAR_WIDTH\tSAMPLE\tLIBRARY\tREAD_GROUP", - "All Reads\tALL\t0\t17252\t23\t11\t0.356565\t0.074349\t\t\t", - "All Reads\tALL\t1\t3503\t13\t13\t0.992552\t0.275284\t\t\t", - "All Reads\tALL\t2\t5640\t19\t10\t0.900999\t0.206703\t\t\t", - "All Reads\tALL\t3\t3475\t11\t11\t0.846618\t0.255265\t\t\t", - "All Reads\tALL\t4\t4275\t7\t9\t0.437937\t0.165525\t\t\t", - "All Reads\tALL\t5\t3480\t3\t9\t0.230564\t0.133116\t\t\t", - "All Reads\tALL\t6\t3400\t5\t11\t0.393315\t0.175896\t\t\t", - "All Reads\tALL\t7\t3235\t12\t8\t0.992103\t0.286395\t\t\t", - "All Reads\tALL\t8\t3640\t10\t10\t0.734765\t0.232353\t\t\t", - "All Reads\tALL\t9\t3412\t6\t16\t0.470319\t0.192007\t\t\t", - "All Reads\tALL\t10\t3608\t10\t9\t0.741282\t0.234414\t\t\t", - "All Reads\tALL\t11\t3699\t6\t11\t0.433827\t0.177109\t\t\t", - "All Reads\tALL\t12\t3840\t9\t8\t0.626846\t0.208949\t\t\t", - "All Reads\tALL\t13\t3874\t17\t11\t1.173651\t0.284652\t\t\t", - "All Reads\tALL\t14\t3693\t17\t10\t1.231174\t0.298604\t\t\t", - "All Reads\tALL\t15\t3986\t29\t10\t1.945855\t0.361336\t\t\t", - "All Reads\tALL\t16\t3911\t25\t10\t1.70963\t0.341926\t\t\t", - "All Reads\tALL\t17\t3778\t29\t10\t2.052986\t0.38123\t\t\t", - "All Reads\tALL\t18\t3793\t28\t10\t1.974354\t0.373118\t\t\t", - "All Reads\tALL\t19\t3698\t35\t10\t2.531343\t0.427875\t\t\t", - "All Reads\tALL\t20\t3735\t34\t10\t2.434659\t0.417541\t\t\t", - "All Reads\tALL\t21\t3759\t31\t9\t2.205663\t0.396149\t\t\t", - "All Reads\tALL\t22\t3461\t42\t10\t3.245619\t0.50081\t\t\t", - "All Reads\tALL\t23\t3475\t39\t10\t3.001647\t0.480648\t\t\t", - "All Reads\tALL\t24\t3393\t50\t10\t3.941268\t0.557379\t\t\t", - "All Reads\tALL\t25\t3365\t54\t10\t4.291988\t0.584066\t\t\t", - "All Reads\tALL\t26\t3200\t52\t10\t4.346135\t0.6027\t\t\t", - "All Reads\tALL\t27\t2988\t54\t10\t4.833514\t0.657758\t\t\t", - "All Reads\tALL\t28\t2852\t46\t10\t4.313782\t0.636032\t\t\t", - "All Reads\tALL\t29\t2805\t47\t11\t4.481412\t0.653681\t\t\t", - "All Reads\tALL\t30\t2833\t18\t10\t1.699322\t0.400534\t\t\t", - "All Reads\tALL\t31\t2731\t36\t9\t3.525581\t0.587597\t\t\t", - "All Reads\tALL\t32\t2760\t42\t10\t4.069959\t0.628008\t\t\t", - "All Reads\tALL\t33\t2776\t20\t9\t1.926905\t0.430869\t\t\t", - "All Reads\tALL\t34\t2475\t20\t10\t2.161248\t0.48327\t\t\t", - "All Reads\tALL\t35\t2672\t16\t9\t1.601524\t0.400381\t\t\t", - "All Reads\tALL\t36\t2796\t8\t11\t0.765249\t0.270556\t\t\t", - "All Reads\tALL\t37\t2850\t18\t11\t1.689186\t0.398145\t\t\t", - "All Reads\tALL\t38\t2826\t20\t10\t1.892813\t0.423246\t\t\t", - "All Reads\tALL\t39\t3054\t10\t10\t0.875751\t0.276937\t\t\t", - "All Reads\tALL\t40\t3449\t9\t9\t0.69791\t0.232637\t\t\t", - "All Reads\tALL\t41\t4012\t19\t9\t1.266609\t0.29058\t\t\t", - "All Reads\tALL\t42\t4971\t14\t8\t0.753241\t0.201312\t\t\t", - "All Reads\tALL\t43\t5630\t5\t8\t0.237526\t0.106225\t\t\t", - "All Reads\tALL\t44\t6409\t5\t11\t0.208655\t0.093314\t\t\t", - "All Reads\tALL\t45\t7297\t5\t10\t0.183263\t0.081958\t\t\t", - "All Reads\tALL\t46\t8146\t2\t11\t0.065665\t0.046432\t\t\t", - "All Reads\tALL\t47\t8876\t3\t12\t0.090397\t0.052191\t\t\t", - "All Reads\tALL\t48\t9213\t0\t0\t0\t0\t\t\t", - "All Reads\tALL\t49\t9815\t7\t12\t0.190747\t0.072096\t\t\t", - "All Reads\tALL\t50\t10134\t5\t8\t0.131959\t0.059014\t\t\t", - "All Reads\tALL\t51\t9913\t6\t9\t0.161881\t0.066088\t\t\t", - "All Reads\tALL\t52\t9189\t1\t0\t0.029106\t0.029106\t\t\t", - "All Reads\tALL\t53\t8455\t3\t10\t0.094898\t0.054789\t\t\t", - "All Reads\tALL\t54\t7312\t4\t14\t0.14631\t0.073155\t\t\t", - "All Reads\tALL\t55\t5984\t1\t6\t0.044695\t0.044695\t\t\t", - "All Reads\tALL\t56\t4790\t2\t11\t0.111672\t0.078964\t\t\t", + "All Reads\tALL\t0\t17252\t54\t12\t0.580825\t0.07904\t\t\t", + "All Reads\tALL\t1\t3503\t16\t11\t0.847561\t0.21189\t\t\t", + "All Reads\tALL\t2\t5640\t36\t11\t1.184444\t0.197407\t\t\t", + "All Reads\tALL\t3\t3475\t24\t11\t1.281585\t0.261602\t\t\t", + "All Reads\tALL\t4\t4275\t18\t11\t0.781317\t0.184158\t\t\t", + "All Reads\tALL\t5\t3480\t10\t10\t0.533227\t0.168621\t\t\t", + "All Reads\tALL\t6\t3400\t8\t12\t0.436619\t0.154368\t\t\t", + "All Reads\tALL\t7\t3235\t21\t11\t1.204581\t0.262861\t\t\t", + "All Reads\tALL\t8\t3640\t16\t10\t0.815661\t0.203915\t\t\t", + "All Reads\tALL\t9\t3412\t9\t11\t0.489468\t0.163156\t\t\t", + "All Reads\tALL\t10\t3608\t20\t10\t1.028619\t0.230006\t\t\t", + "All Reads\tALL\t11\t3699\t13\t10\t0.652154\t0.180875\t\t\t", + "All Reads\tALL\t12\t3840\t15\t9\t0.724855\t0.187157\t\t\t", + "All Reads\tALL\t13\t3874\t28\t10\t1.341187\t0.253461\t\t\t", + "All Reads\tALL\t14\t3693\t28\t10\t1.406921\t0.265883\t\t\t", + "All Reads\tALL\t15\t3986\t37\t10\t1.722485\t0.283175\t\t\t", + "All Reads\tALL\t16\t3911\t52\t11\t2.467213\t0.342141\t\t\t", + "All Reads\tALL\t17\t3778\t43\t10\t2.112018\t0.32208\t\t\t", + "All Reads\tALL\t18\t3793\t38\t10\t1.859053\t0.301578\t\t\t", + "All Reads\tALL\t19\t3698\t42\t10\t2.107528\t0.325199\t\t\t", + "All Reads\tALL\t20\t3735\t46\t10\t2.285379\t0.336961\t\t\t", + "All Reads\tALL\t21\t3759\t40\t9\t1.974598\t0.312211\t\t\t", + "All Reads\tALL\t22\t3461\t54\t10\t2.895231\t0.393991\t\t\t", + "All Reads\tALL\t23\t3475\t55\t10\t2.936966\t0.39602\t\t\t", + "All Reads\tALL\t24\t3393\t61\t10\t3.336085\t0.427142\t\t\t", + "All Reads\tALL\t25\t3365\t73\t10\t4.025584\t0.471159\t\t\t", + "All Reads\tALL\t26\t3200\t67\t10\t3.885223\t0.474655\t\t\t", + "All Reads\tALL\t27\t2988\t60\t10\t3.726162\t0.481045\t\t\t", + "All Reads\tALL\t28\t2852\t51\t10\t3.31827\t0.464651\t\t\t", + "All Reads\tALL\t29\t2805\t57\t11\t3.770796\t0.499454\t\t\t", + "All Reads\tALL\t30\t2833\t35\t9\t2.292517\t0.387506\t\t\t", + "All Reads\tALL\t31\t2731\t39\t9\t2.649927\t0.424328\t\t\t", + "All Reads\tALL\t32\t2760\t43\t10\t2.891016\t0.440876\t\t\t", + "All Reads\tALL\t33\t2776\t32\t9\t2.139053\t0.378135\t\t\t", + "All Reads\tALL\t34\t2475\t23\t9\t1.724423\t0.359567\t\t\t", + "All Reads\tALL\t35\t2672\t21\t10\t1.458391\t0.318247\t\t\t", + "All Reads\tALL\t36\t2796\t12\t10\t0.796407\t0.229903\t\t\t", + "All Reads\tALL\t37\t2850\t23\t10\t1.497525\t0.312256\t\t\t", + "All Reads\tALL\t38\t2826\t27\t10\t1.772894\t0.341194\t\t\t", + "All Reads\tALL\t39\t3054\t9\t10\t0.546845\t0.182282\t\t\t", + "All Reads\tALL\t40\t3449\t11\t10\t0.591821\t0.178441\t\t\t", + "All Reads\tALL\t41\t4012\t29\t8\t1.341307\t0.249074\t\t\t", + "All Reads\tALL\t42\t4971\t20\t9\t0.746582\t0.166941\t\t\t", + "All Reads\tALL\t43\t5630\t7\t9\t0.230718\t0.087203\t\t\t", + "All Reads\tALL\t44\t6409\t9\t12\t0.260581\t0.08686\t\t\t", + "All Reads\tALL\t45\t7297\t7\t10\t0.17801\t0.067282\t\t\t", + "All Reads\tALL\t46\t8146\t4\t12\t0.091119\t0.045559\t\t\t", + "All Reads\tALL\t47\t8876\t8\t13\t0.167249\t0.059131\t\t\t", + "All Reads\tALL\t48\t9213\t4\t7\t0.080566\t0.040283\t\t\t", + "All Reads\tALL\t49\t9815\t14\t10\t0.264685\t0.07074\t\t\t", + "All Reads\tALL\t50\t10134\t17\t8\t0.311286\t0.075498\t\t\t", + "All Reads\tALL\t51\t9913\t16\t7\t0.299506\t0.074877\t\t\t", + "All Reads\tALL\t52\t9189\t6\t12\t0.121164\t0.049465\t\t\t", + "All Reads\tALL\t53\t8455\t6\t11\t0.131683\t0.053759\t\t\t", + "All Reads\tALL\t54\t7312\t7\t14\t0.177645\t0.067143\t\t\t", + "All Reads\tALL\t55\t5984\t3\t8\t0.09303\t0.053711\t\t\t", + "All Reads\tALL\t56\t4790\t4\t9\t0.154959\t0.077479\t\t\t", "All Reads\tALL\t57\t3659\t0\t0\t0\t0\t\t\t", - "All Reads\tALL\t58\t2618\t1\t7\t0.10216\t0.10216\t\t\t", - "All Reads\tALL\t59\t1766\t2\t8\t0.302893\t0.214178\t\t\t", + "All Reads\tALL\t58\t2618\t3\t7\t0.212639\t0.122767\t\t\t", + "All Reads\tALL\t59\t1766\t4\t8\t0.420301\t0.21015\t\t\t", "All Reads\tALL\t60\t1281\t0\t0\t0\t0\t\t\t", "All Reads\tALL\t61\t837\t0\t0\t0\t0\t\t\t", "All Reads\tALL\t62\t441\t0\t0\t0\t0\t\t\t", @@ -608,18 +558,18 @@ "alignment_metrics", [ "CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tSD_READ_LENGTH\tMEDIAN_READ_LENGTH\tMAD_READ_LENGTH\tMIN_READ_LENGTH\tMAX_READ_LENGTH\tMEAN_ALIGNED_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER\tPCT_SOFTCLIP\tPCT_HARDCLIP\tAVG_POS_3PRIME_SOFTCLIP_LENGTH\tSAMPLE\tLIBRARY\tREAD_GROUP", - "FIRST_OF_PAIR\t716\t582\t0.812849\t0\t407\t0.699313\t28491\t194\t13413\t12766\t0\t0.096131\t0.093769\t0.004422\t75.266323\t4.431486\t76\t0\t32\t76\t49.16323\t219\t0.538084\t271\t0.665848\t0\t0.916462\t0.01676\t0\t0.043465\t0\t16.052632\t\t\t", - "SECOND_OF_PAIR\t716\t582\t0.812849\t0\t394\t0.676976\t27177\t192\t13181\t12115\t0\t0.089641\t0.086065\t0.003716\t75.314433\t4.360963\t76\t0\t32\t76\t46.883162\t219\t0.555838\t258\t0.654822\t0\t0.086294\t0.016854\t0\t0.052175\t0\t16.28\t\t\t", - "PAIR\t1432\t1164\t0.812849\t0\t801\t0.688144\t55668\t386\t26594\t24881\t0\t0.092977\t0.089968\t0.004078\t75.290378\t4.394542\t76\t0\t32\t76\t48.023196\t438\t0.546816\t529\t0.660424\t0\t0.508115\t0.016807\t0\t0.047822\t0\t16.181818\t\t\t" + "FIRST_OF_PAIR\t899\t607\t0.675195\t0\t493\t0.812191\t32309\t302\t19684\t18772\t3\t0.103312\t0.098954\t0.004364\t74.663921\t5.91042\t76\t0\t31\t76\t53.443163\t348\t0.705882\t156\t0.31643\t0\t0.89858\t0.010101\t0\t0.093312\t0\t15.835294\t\t\t", + "SECOND_OF_PAIR\t899\t607\t0.675195\t0\t462\t0.76112\t30277\t299\t19999\t18469\t3\t0.102474\t0.09557\t0.004096\t74.710049\t5.864669\t76\t0\t31\t76\t50.116969\t348\t0.753247\t125\t0.270563\t0\t0.112554\t0.010453\t0\t0.086176\t0\t14.56701\t\t\t", + "PAIR\t1798\t1214\t0.675195\t0\t955\t0.786656\t62586\t601\t39683\t37241\t3\t0.102909\t0.097258\t0.004234\t74.686985\t5.885207\t76\t0\t31\t76\t51.780066\t696\t0.728796\t281\t0.294241\t0\t0.518325\t0.010274\t0\t0.089743\t0\t15.159341\t\t\t" ] ], [ "methyldackel_extract", - "598a03b683510eec51cbb7f3838f5e01" + "d57eb8ceac1110d8e3562a1419203c1b" ], [ "mbias", - "7affa90a76867245b02b8197f0c69e92" + "0e205776d3925fd9fd3b5f4cba76092d" ], [ "nonconverted", @@ -637,9 +587,23 @@ "positional_summary", [ "methylkit_file\tchr\ttarget_length\tposition\tcontext\tmean_methylation\tn_loci\tn_measurements", + "emseq-test1\tchr1\t204\t90\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t182\t95\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t182\t81\tCHH\t0\t1\t1", "emseq-test1\tchr1\t151\t142\tCG\t100\t1\t1", - "emseq-test1\tchr1\t182\t178\tCG\t0\t1\t1", - "emseq-test1\tchr1\t204\t189\tCG\t0\t1\t1" + "emseq-test1\tchr1\t204\t94\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t204\t80\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t204\t92\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t182\t83\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t204\t102\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t182\t178\tCG\t14.2857\t1\t1", + "emseq-test1\tchr1\t204\t106\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t204\t74\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t182\t79\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t182\t63\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t204\t189\tCG\t14.2857\t1\t1", + "emseq-test1\tchr1\t182\t69\tCHH\t0\t1\t1", + "emseq-test1\tchr1\t182\t91\tCHH\t0\t1\t1" ] ], [ @@ -650,8 +614,10 @@ "region_summary", [ "library\ttarget_locus\ttarget_name\tcontext\tmean_methylation", - "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCG\t0", - "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCG\t0", + "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCG\t14.2857", + "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCHH\t0", + "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCG\t14.2857", + "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCHH\t0", "emseq-test2\tchr1:31717-31868\tStemLoop_31767_31817_2mm_18C_0CG\tCG\t100" ] ], @@ -660,8 +626,22 @@ [ "methylkit_file\tchr\tstart\tend\tcontext\tmethylation\ttarget_locus\ttarget_name", "emseq-test2\tchr1\t31858\t31859\tCG\t100\tchr1:31718-31868\tStemLoop_31767_31817_2mm_18C_0CG", - "emseq-test2\tchr1\t141027\t141028\tCG\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", - "emseq-test2\tchr1\t141027\t141028\tCG\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG" + "emseq-test2\tchr1\t140912\t140913\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t140918\t140919\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t140928\t140929\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t140930\t140931\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t140932\t140933\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t140940\t140941\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t140944\t140945\tCHH\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t141027\t141028\tCG\t14.2857\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG", + "emseq-test2\tchr1\t140912\t140913\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", + "emseq-test2\tchr1\t140918\t140919\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", + "emseq-test2\tchr1\t140928\t140929\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", + "emseq-test2\tchr1\t140930\t140931\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", + "emseq-test2\tchr1\t140932\t140933\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", + "emseq-test2\tchr1\t140940\t140941\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", + "emseq-test2\tchr1\t140944\t140945\tCHH\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG", + "emseq-test2\tchr1\t141027\t141028\tCG\t14.2857\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG" ] ], [ @@ -695,9 +675,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.6" }, - "timestamp": "2025-09-17T10:23:29.040913733" + "timestamp": "2026-07-02T13:46:20.69713408" } } \ No newline at end of file