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# MultiQC search patterns.
# Default configurations for how modules can find their log files.
# Loaded by the config module so that these patterns can be overwritten in user config files.
adapterRemoval:
fn: '*.settings'
contents: 'AdapterRemoval'
num_lines: 1
afterqc:
fn: '*.json'
contents: 'allow_mismatch_in_poly'
bamtools/stats:
contents: 'Stats for BAM file(s):'
shared: true
num_lines: 2
bbmap/stats:
contents: '#Name Reads ReadsPct'
num_lines: 4
bbmap/aqhist:
contents: '#Quality count1 fraction1 count2 fraction2'
num_lines: 1
bbmap/bhist:
contents: '#Pos A C G T N'
num_lines: 1
bbmap/bincov:
# 3rd line (1st is #Mean)
contents: '#RefName Cov Pos RunningPos'
num_lines: 3
bbmap/bqhist:
contents: '#BaseNum count_1 min_1 max_1 mean_1 Q1_1 med_1 Q3_1 LW_1 RW_1 count_2 min_2 max_2 mean_2 Q1_2 med_2 Q3_2 LW_2 RW_2'
num_lines: 1
bbmap/covhist:
contents: '#Coverage numBases'
num_lines: 1
bbmap/covstats:
contents: '#ID Avg_fold'
num_lines: 1
bbmap/ehist:
contents: '#Errors Count'
num_lines: 1
bbmap/gchist:
# 5th line (1st is #Mean)
contents: '#GC Count'
num_lines: 5
bbmap/idhist:
contents: '#Mean_reads'
num_lines: 1
bbmap/ihist:
# 6th line (first is #Mean)
contents: '#InsertSize Count'
num_lines: 6
bbmap/indelhist:
contents: '#Length Deletions Insertions'
num_lines: 1
bbmap/lhist:
contents: '#Length Count'
num_lines: 1
bbmap/mhist:
contents: '#BaseNum Match1 Sub1 Del1 Ins1 N1 Other1 Match2 Sub2 Del2 Ins2 N2 Other2'
num_lines: 1
bbmap/qahist:
contents: '#Deviation'
num_lines: 1
bbmap/qhist:
contents: '#BaseNum Read1_linear Read1_log Read1_measured Read2_linear Read2_log Read2_measured'
num_lines: 1
bbmap/rpkm:
contents: '#File '
num_lines: 1
bbmap/statsfile_machine:
contents: 'Reads Used='
num_lines: 1
bbmap/statsfile:
contents: 'Reads Used:'
num_lines: 1
bcftools/stats:
contents: 'This file was produced by bcftools stats'
shared: true
bcl2fastq:
- fn: 'Stats.json'
contents: 'DemuxResults'
- num_lines: 300
biobloomtools:
contents: 'filter_id hits misses shared rate_hit rate_miss rate_shared'
num_lines: 2
bismark/align:
fn: '*_[SP]E_report.txt'
bismark/dedup:
fn: '*.deduplication_report.txt'
bismark/meth_extract:
fn: '*_splitting_report.txt'
bismark/m_bias:
fn: '*M-bias.txt'
bismark/bam2nuc:
fn: '*.nucleotide_stats.txt'
bowtie1:
contents: '# reads processed:'
exclude_fn:
# Tophat log files
- 'bowtie.left_kept_reads.log'
- 'bowtie.left_kept_reads.m2g_um.log'
- 'bowtie.left_kept_reads.m2g_um_seg1.log'
- 'bowtie.left_kept_reads.m2g_um_seg2.log'
- 'bowtie.right_kept_reads.log'
- 'bowtie.right_kept_reads.m2g_um.log'
- 'bowtie.right_kept_reads.m2g_um_seg1.log'
- 'bowtie.right_kept_reads.m2g_um_seg2.log'
shared: true
bowtie2:
contents: 'reads; of these:'
exclude_contents:
- 'bisulfite'
- 'HiC-Pro'
shared: true
busco:
fn: 'short_summary_*'
contents: 'BUSCO version is:'
num_lines: 1
custom_content:
fn_re: '.+_mqc\.(yaml|yml|json|txt|csv|tsv|log|out)'
clipandmerge:
contents: 'ClipAndMerge ('
num_lines: 5
clusterflow/logs:
fn: '*_clusterFlow.txt'
shared: true
clusterflow/runfiles:
fn: '*.run'
contents: 'Cluster Flow Run File'
num_lines: 2
conpair/concordance:
contents: 'markers (coverage per marker threshold : '
num_lines: 3
conpair/contamination:
contents: 'Tumor sample contamination level: '
num_lines: 3
cutadapt:
contents: 'This is cutadapt'
# contents: 'cutadapt version' # Use this instead if using very old versions of cutadapt (eg. v1.2)
shared: true
dedup:
fn: 'dedup.log'
deeptools/bamPEFragmentSize:
contents: ' Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu.'
num_lines: 1
deeptools/estimateReadFiltering:
contents: 'Sample Total Reads Mapped Reads Alignments in blacklisted regions Estimated mapped reads'
num_lines: 1
deeptools/plotCoverageStdout:
contents: 'sample mean std min 25% 50% 75% max'
num_lines: 1
deeptools/plotCoverageOutRawCounts:
contents: "#plotCoverage --outRawCounts"
num_lines: 1
deeptools/plotEnrichment:
contents: 'file featureType percent featureReadCount totalReadCount'
num_lines: 1
deeptools/plotFingerprintOutRawCounts:
contents: '#plotFingerprint --outRawCounts'
num_lines: 1
deeptools/plotFingerprintOutQualityMetrics:
contents: 'Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point'
num_lines: 1
fastp:
fn: '*fastp.json'
fastq_screen:
fn: '*_screen.txt'
fastqc/data:
fn: 'fastqc_data.txt'
fastqc/zip:
fn: '*_fastqc.zip'
fastqc/theoretical_gc:
fn: '*fastqc_theoretical_gc*'
featurecounts:
fn: '*.summary'
shared: true
flexbar:
contents: 'Flexbar - flexible barcode and adapter removal'
shared: true
gatk/varianteval:
contents: '#:GATKTable:TiTvVariantEvaluator'
shared: true
gatk/base_recalibrator:
contents: '#:GATKTable:Arguments:Recalibration'
num_lines: 3
goleft_indexcov/roc:
fn: '*-indexcov.roc'
goleft_indexcov/ped:
fn: '*-indexcov.ped'
happy:
fn: '*.summary.csv'
contents: 'Type,Filter,TRUTH'
htseq:
contents: '__too_low_aQual'
hicexplorer:
contents: 'Min rest. site distance'
max_filesize: 4096
num_lines: 5
hicup:
fn: 'HiCUP_summary_report*'
hicpro/mmapstat:
fn: '*.mmapstat'
hicpro/mpairstat:
fn: '*.mpairstat'
hicpro/mergestat:
fn: '*.mergestat'
hicpro/mRSstat:
fn: '*.mRSstat'
hicpro/assplit:
fn: '*.assplit.stat'
hisat2:
contents: 'HISAT2 summary stats:'
shared: true
homer/findpeaks:
contents: '# HOMER Peaks'
num_lines: 3
homer/GCcontent:
fn: 'tagGCcontent.txt'
homer/genomeGCcontent:
fn: 'genomeGCcontent.txt'
homer/RestrictionDistribution:
fn: 'petagRestrictionDistribution.*.txt'
homer/LengthDistribution:
fn: 'tagLengthDistribution.txt'
homer/tagInfo:
fn: 'tagInfo.txt'
homer/FreqDistribution:
fn: 'petag.FreqDistribution_1000.txt'
interop/summary:
contents: 'Level,Yield,Projected Yield,Aligned,Error Rate,Intensity C1,%>=Q30'
interop/index-summary:
contents: 'Total Reads,PF Reads,% Read Identified (PF),CV,Min,Max'
jellyfish:
fn: '*_jf.hist'
kallisto:
contents: '[quant] finding pseudoalignments for the reads'
shared: true
kat:
fn: '*.dist_analysis.json'
leehom:
contents: 'Adapter dimers/chimeras'
shared: true
longranger/summary:
fn: '*summary.csv'
contents: 'longranger_version,instrument_ids,gems_detected,mean_dna_per_gem,bc_on_whitelist,bc_mean_qscore,n50_linked_reads_per_molecule'
num_lines: 2
longranger/invocation:
fn: '_invocation'
contents: 'call PHASER_SVCALLER_CS('
max_filesize: 2048
macs2:
fn: '*_peaks.xls'
methylQA:
fn: '*.report'
shared: true
mirtrace/summary:
fn: 'mirtrace-results.json'
mirtrace/length:
fn: 'mirtrace-stats-length.tsv'
mirtrace/contaminationbasic:
fn: 'mirtrace-stats-contamination_basic.tsv'
mirtrace/mirnacomplexity:
fn: 'mirtrace-stats-mirna-complexity.tsv'
disambiguate:
contents: 'unique species A pairs'
num_lines: 2
peddy/summary_table:
fn: '*.peddy.ped'
peddy/het_check:
fn: '*.het_check.csv'
peddy/ped_check:
fn: '*.ped_check.csv'
peddy/sex_check:
fn: '*.sex_check.csv'
peddy/background_pca:
fn: '*.background_pca.json'
picard/alignment_metrics:
contents: 'AlignmentSummaryMetrics'
shared: true
picard/basedistributionbycycle:
contents: 'BaseDistributionByCycleMetrics'
shared: true
picard/gcbias:
contents: 'GcBias'
shared: true
picard/hsmetrics:
contents: 'HsMetrics'
shared: true
picard/insertsize:
contents: 'InsertSizeMetrics'
shared: true
picard/markdups:
contents: 'DuplicationMetrics'
shared: true
picard/oxogmetrics:
contents: 'CollectOxoGMetrics'
shared: true
picard/pcr_metrics:
contents: 'TargetedPcrMetrics'
shared: true
picard/rnaseqmetrics:
contents_re: 'Collect[Rr]na[Ss]eq[Mm]etrics'
shared: true
picard/rrbs_metrics:
contents: 'RrbsSummaryMetrics'
shared: true
picard/sam_file_validation:
fn: '*[Vv]alidate[Ss]am[Ff]ile*'
picard/wgs_metrics:
contents: 'CollectWgsMetrics'
shared: true
preseq:
- contents: 'EXPECTED_DISTINCT'
num_lines: 2
- contents: 'distinct_reads'
num_lines: 2
preseq/real_counts:
fn: '*preseq_real_counts*'
prokka:
contents: 'contigs:'
num_lines: 2
qorts:
contents: 'BENCHMARK_MinutesOnSamIteration'
num_lines: 100
qualimap/bamqc/genome_results:
fn: 'genome_results.txt'
qualimap/bamqc/coverage:
fn: 'coverage_histogram.txt'
qualimap/bamqc/insert_size:
fn: 'insert_size_histogram.txt'
qualimap/bamqc/genome_fraction:
fn: 'genome_fraction_coverage.txt'
qualimap/bamqc/gc_dist:
fn: 'mapped_reads_gc-content_distribution.txt'
qualimap/rnaseq/rnaseq_results:
fn: 'rnaseq_qc_results.txt'
qualimap/rnaseq/coverage:
fn: 'coverage_profile_along_genes_(total).txt'
quast:
fn: 'report.tsv'
shared: true
rna_seqc/metrics:
fn: 'metrics.tsv'
shared: true
rna_seqc/coverage:
fn_re: 'meanCoverageNorm_(high|medium|low)\.txt'
rna_seqc/correlation:
fn_re: 'corrMatrix(Pearson|Spearman)\.txt'
rsem:
- fn: '*.cnt'
rseqc/bam_stat:
contents: 'Proper-paired reads map to different chrom:'
max_filesize: 500000
rseqc/gene_body_coverage:
fn: '*.geneBodyCoverage.txt'
rseqc/inner_distance:
fn: '*.inner_distance_freq.txt'
rseqc/junction_annotation:
contents: 'Partial Novel Splicing Junctions:'
max_filesize: 500000
rseqc/junction_saturation:
fn: '*.junctionSaturation_plot.r'
rseqc/read_gc:
fn: '*.GC.xls'
rseqc/read_distribution:
contents: 'Group Total_bases Tag_count Tags/Kb'
max_filesize: 500000
rseqc/read_duplication_pos:
fn: '*.pos.DupRate.xls'
rseqc/infer_experiment:
- fn: '*infer_experiment.txt'
- contents: 'Fraction of reads explained by'
max_filesize: 500000
salmon/meta:
fn: 'meta_info.json'
contents: 'salmon_version'
salmon/fld:
fn: 'flenDist.txt'
samblaster:
contents: 'samblaster: Version'
shared: true
samtools/stats:
contents: 'This file was produced by samtools stats'
shared: true
samtools/flagstat:
contents: 'in total (QC-passed reads + QC-failed reads)'
shared: true
samtools/idxstats:
fn: '*idxstat*'
samtools/rmdup:
contents: '[bam_rmdup'
shared: true
sargasso:
fn: 'overall_filtering_summary.txt'
skewer:
contents: 'maximum error ratio allowed (-r):'
shared: true
slamdunk/summary:
contents: '# slamdunk summary'
num_lines: 1
slamdunk/PCA:
contents: '# slamdunk PCA'
num_lines: 1
slamdunk/rates:
contents: '# slamdunk rates'
num_lines: 1
slamdunk/utrrates:
contents: '# slamdunk utrrates'
num_lines: 1
slamdunk/tcperreadpos:
contents: '# slamdunk tcperreadpos'
num_lines: 1
slamdunk/tcperutrpos:
contents: '# slamdunk tcperutr'
num_lines: 1
snpeff:
contents: 'SnpEff_version'
max_filesize: 1000000
sortmerna:
contents: 'Minimal SW score based on E-value'
shared: true
star:
fn: '*Log.final.out'
star/genecounts:
fn: '*ReadsPerGene.out.tab'
supernova/report:
fn: '*report*.txt'
num_lines: 100
contents: '- assembly checksum ='
supernova/summary:
fn: 'summary.json'
num_lines: 120
contents: '"lw_mean_mol_len":'
supernova/molecules:
fn: 'histogram_molecules.json'
num_lines: 10
contents: '"description": "molecules",'
supernova/kmers:
fn: 'histogram_kmer_count.json'
num_lines: 10
contents: '"description": "kmer_count",'
theta2:
fn: '*.BEST.results'
tophat:
fn: '*align_summary.txt'
shared: true
trimmomatic:
contents: 'Trimmomatic'
shared: true
vcftools/relatedness2:
fn: '*.relatedness2'
vcftools/tstv_by_count:
fn: '*.TsTv.count'
vcftools/tstv_by_qual:
fn: '*.TsTv.qual'
vcftools/tstv_summary:
fn: '*.TsTv.summary'
verifybamid/selfsm:
fn: '*.selfSM'