diff --git a/conf/base.config b/conf/base.config index ac62b1efd..d0e3599cb 100644 --- a/conf/base.config +++ b/conf/base.config @@ -85,6 +85,11 @@ process { errorStrategy = { task.exitStatus in [141] ? 'ignore' : 'retry' } } + // Add 1 retry for certain java tools as not enough heap space java errors gives exit code 1 + withName: dedup { + errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' } + } + // Add 1 retry as not enough heapspace java error gives exit code 1 withName: malt { errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' } diff --git a/docs/images/output/bowtie2/bowtie2_alignment_scores.png b/docs/images/output/bowtie2/bowtie2_alignment_scores.png new file mode 100644 index 000000000..e26969924 Binary files /dev/null and b/docs/images/output/bowtie2/bowtie2_alignment_scores.png differ diff --git a/docs/images/output/bowtie2/bowtie2_alignment_scores.svg b/docs/images/output/bowtie2/bowtie2_alignment_scores.svg new file mode 100644 index 000000000..08ce50d6d --- /dev/null +++ b/docs/images/output/bowtie2/bowtie2_alignment_scores.svg @@ -0,0 +1,2487 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + Beautiful! Many uniquely mapping reads, indicating well-preserved high-endogenous sample! Go have a tea-break! + Okay for low endogenous aDNA! Few reads mapping, but mostly unique! + Warning! Many reads map in multiple places - possibly lots of low complexity reads! + + + + Number of reads + Bowtie 2: Alignment scores + ZandraSelina + + + + Sample + + + + + + + + + + Number of reads + Sample + + + + + + + + + + + + + + + + + + Number of reads + Sample + + + + + + + + + + + + Mapped uniquely + + Multimapped + + Not aligned + CC-BY 4.0 + + + diff --git a/docs/images/output/multivcfanalyzer/multivcfanalyzer_call_categories.png b/docs/images/output/multivcfanalyzer/multivcfanalyzer_call_categories.png new file mode 100644 index 000000000..eabf5ec41 Binary files /dev/null and b/docs/images/output/multivcfanalyzer/multivcfanalyzer_call_categories.png differ diff --git a/docs/images/output/multivcfanalyzer/multivcfanalyzer_call_categories.svg b/docs/images/output/multivcfanalyzer/multivcfanalyzer_call_categories.svg new file mode 100644 index 000000000..697641992 --- /dev/null +++ b/docs/images/output/multivcfanalyzer/multivcfanalyzer_call_categories.svg @@ -0,0 +1,2375 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + Number of positions + MultiVCFAnalyzer: Call categories + ZandraSelina + + Sample + + + + + + SNP calls (hom) + + SNPcalls (het) + CC-BY 4.0 + + + Number of positions + Sample + + + + Warning, many het. SNP calls may indicate cross-mapping, or high damage in low coverage data! + + Normal for low coverage aDNA, with many discarded SNP calls! Reward yourself by looking at photos of axolotls! + + + + + + + SNP calls (hom) + + Reference calls + + Discarded SNP call + + + + + + + + diff --git a/docs/images/output/picard/picard_deduplication_stats.png b/docs/images/output/picard/picard_deduplication_stats.png new file mode 100644 index 000000000..d673da3d8 Binary files /dev/null and b/docs/images/output/picard/picard_deduplication_stats.png differ diff --git a/docs/images/output/picard/picard_deduplication_stats.svg b/docs/images/output/picard/picard_deduplication_stats.svg new file mode 100644 index 000000000..32266c746 --- /dev/null +++ b/docs/images/output/picard/picard_deduplication_stats.svg @@ -0,0 +1,2398 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + Number of reads + Picard: Deduplication stats + ZandraSelina + + Sample + + + + + + Unique + + Duplicate + + Unmapped + CC-BY 4.0 + + + + + + Number of reads + Sample + + + + + + + + + + + + + + + Beautiful for aDNA - few mapped reads, but mostly unique! Go reward yourself with a bratwurst! + + Warning! Lots of duplicates, will inflate coverage and give false confidence in variant calling! + + + diff --git a/docs/images/output/sexdeterrmine/sexdeterrmine_relative_coverage.png b/docs/images/output/sexdeterrmine/sexdeterrmine_relative_coverage.png new file mode 100644 index 000000000..e3f72dee1 Binary files /dev/null and b/docs/images/output/sexdeterrmine/sexdeterrmine_relative_coverage.png differ diff --git a/docs/images/output/sexdeterrmine/sexdeterrmine_relative_coverage.svg b/docs/images/output/sexdeterrmine/sexdeterrmine_relative_coverage.svg new file mode 100644 index 000000000..7a4edb746 --- /dev/null +++ b/docs/images/output/sexdeterrmine/sexdeterrmine_relative_coverage.svg @@ -0,0 +1,2335 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + X + SexDetErrmine: Relative coverage + ZandraSelina + + Y + CC-BY 4.0 + Beautiful, clean biological sex determination! Go reward yourself by playing some Zelda! + + Normal for aDNA, biological sex not clear for all individuals - maybe low coverage or contamination? + 0 + 0.5 + 1 + + + + + + + + + + + X + Y + 0 + 0.5 + 1 + + + + + + + + + + + + + diff --git a/main.nf b/main.nf index ee4a26d66..0831b7a97 100644 --- a/main.nf +++ b/main.nf @@ -298,7 +298,7 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome exit 1, "[nf-core/eager] error: the provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}." } -// Mapper sanity checking +// Mapper validation if (params.mapper != 'bwaaln' && !params.mapper == 'circularmapper' && !params.mapper == 'bwamem' && !params.mapper == "bowtie2"){ exit 1, "[nf-core/eager] error: invalid mapper option. Options are: 'bwaaln', 'bwamem', 'circularmapper', 'bowtie2'. Default: 'bwaaln'. You gave: --mapper '${params.mapper}'." } @@ -353,7 +353,7 @@ if (!has_extension(params.input, "tsv") && params.skip_collapse && params.singl exit 1, "[nf-core/eager] error: --skip_collapse can only be set for paired_end samples." } -// Strip mode sanity checking +// Strip mode validation if (params.strip_input_fastq){ if (!(['strip','replace'].contains(params.strip_mode))) { exit 1, "[nf-core/eager] error: --strip_mode can only be set to strip or replace." @@ -364,12 +364,12 @@ if (params.bam_discard_unmapped && params.bam_unmapped_type == '') { exit 1, "[nf-core/eager] error: please specify valid unmapped read output format. Options: 'discard', 'bam', 'fastq', 'both'. You gave --bam_unmapped_type '${params.bam_unmapped_type}'." } -// Bedtools sanity checking +// Bedtools validation if(params.run_bedtools_coverage && params.anno_file == ''){ exit 1, "[nf-core/eager] error: you have turned on bedtools coverage, but not specified a BED or GFF file with --anno_file. Please validate your parameters." } -// BAM filtering sanity checking +// BAM filtering validation if (!params.run_bam_filtering && params.bam_mapping_quality_threshold != 0) { exit 1, "[nf-core/eager] error: please turn on BAM filtering if you want to perform mapping quality filtering! Give --run_bam_filtering." } @@ -386,12 +386,12 @@ if (params.run_bam_filtering && !params.bam_discard_unmapped && params.bam_unmap exit 1, "[nf-core/eager] error: Please turned on unmapped read discarding, if you have specifed a different unmapped type. Give: --bam_discard_unmapped." } -// Deduplication sanity checking +// Deduplication validation if (params.dedupper != 'dedup' && params.dedupper != 'markduplicates') { exit 1, "[nf-core/eager] error: Selected deduplication tool is not recognised. Options: 'dedup' or 'markduplicates'. You gave: --dedupper '${params.dedupper}'." } -// Genotyping sanity checking +// Genotyping validation if (params.run_genotyping){ if (params.genotyping_tool != 'ug' && params.genotyping_tool != 'hc' && params.genotyping_tool != 'freebayes' && params.genotyping_tool != 'pileupcaller' && params.genotyping_tool != 'angsd' ) { exit 1, "[nf-core/eager] error: please specify a genotyper. Options: 'ug', 'hc', 'freebayes', 'pileupcaller'. You gave: --genotyping_tool '${params.genotyping_tool}'." @@ -450,7 +450,7 @@ if (params.run_genotyping){ } } -// Consensus sequence generation sanity checking +// Consensus sequence generation validation if (params.run_vcf2genome) { if (!params.run_genotyping) { exit 1, "[nf-core/eager] error: consensus sequence generation requires genotyping via UnifiedGenotyper on be turned on with the parameter --run_genotyping and --genotyping_tool 'ug'. Please check your genotyping parameters." @@ -461,7 +461,7 @@ if (params.run_vcf2genome) { } } -// MultiVCFAnalyzer sanity checking +// MultiVCFAnalyzer validation if (params.run_multivcfanalyzer) { if (!params.run_genotyping) { exit 1, "[nf-core/eager] error: MultiVCFAnalyzer requires genotyping to be turned on with the parameter --run_genotyping. Please check your genotyping parameters." @@ -476,7 +476,7 @@ if (params.run_multivcfanalyzer) { } } -// Metagenomic sanity checking +// Metagenomic validation if (params.run_metagenomic_screening) { if ( !params.bam_discard_unmapped ) { exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_discard_unmapped and --bam_unmapped_type 'fastq'." @@ -519,7 +519,7 @@ if (params.run_metagenomic_screening) { } } -// MaltExtract Sanity checking +// MaltExtract validation if (params.run_maltextract) { if (params.run_metagenomic_screening && params.metagenomic_tool != 'malt') { @@ -548,7 +548,7 @@ if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) { } if (workflow.profile.contains('awsbatch')) { - // AWSBatch sanity checking + // AWSBatch validation if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch." // Check outdir paths to be S3 buckets if running on AWSBatch // related: https://github.com/nextflow-io/nextflow/issues/813 @@ -1802,7 +1802,7 @@ process dedup{ mv ${bam} ${libraryid}.bam fi - dedup -i ${libraryid}.bam $treat_merged -o . -u + dedup -Xmx${task.memory.toGiga()}g -i ${libraryid}.bam $treat_merged -o . -u mv *.log dedup.log samtools sort -@ ${task.cpus} "${libraryid}"_rmdup.bam -o "${libraryid}"_rmdup.bam samtools index "${size}" "${libraryid}"_rmdup.bam @@ -1814,7 +1814,7 @@ process dedup{ mv ${bam} ${libraryid}.bam fi - dedup -i ${libraryid}.bam $treat_merged -o . -u + dedup -Xmx${task.memory.toGiga()}g -i ${libraryid}.bam $treat_merged -o . -u mv *.log dedup.log samtools sort -@ ${task.cpus} "${libraryid}"_rmdup.bam -o "${libraryid}"_rmdup.bam samtools index "${size}" "${libraryid}"_rmdup.bam @@ -3058,11 +3058,11 @@ workflow.onComplete { log.info "[nf-core/eager] Sent summary e-mail to $email_address (sendmail)" } catch (all) { // Catch failures and try with plaintext - if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) { - [ 'mail', '-s', subject, email_address, '-A', mqc_report ].execute() << email_txt - } else { - [ 'mail', '-s', subject, email_address ].execute() << email_txt + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text', email_address ] + if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) { + mail_cmd += [ '-A', mqc_report ] } + mail_cmd.execute() << email_txt log.info "[nf-core/eager] Sent summary e-mail to $email_address (mail)" } } @@ -3163,6 +3163,9 @@ def extract_data(tsvFile) { def r2 = row.R2.matches('NA') ? 'NA' : return_file(row.R2) def bam = row.BAM.matches('NA') ? 'NA' : return_file(row.BAM) + // check no empty metadata fields + if (samplename == '' || libraryid == '' || lane == '' || colour == '' || seqtype == '' || seqtype == '' || udg == '' || r1 == '' || r2 == '') exit 1, "[nf-core/eager] error: a field does not contain any information. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}" + // Check no 'empty' rows if (r1.matches('NA') && r2.matches('NA') && bam.matches('NA') && bai.matches('NA')) exit 1, "[nf-core/eager] error: A row in your TSV appears to have all files defined as NA. See --help or documentation under 'running the pipeline' for more information. Check row for: ${samplename}" @@ -3239,7 +3242,7 @@ def retrieve_input_paths(input, colour_chem, pe_se, ds_ss, udg_treat, bam_in) { Channel .fromFilePairs( input ) .filter { it =~/.*.fastq.gz|.*.fq.gz|.*.fastq|.*.fq/ } - .ifEmpty { exit 1, "[nf-core/eager] error: Your specified FASTQ read files did not end in: '.fastq.gz', '.fq.gz', '.fastq', or '.fq' " } + .ifEmpty { exit 1, "[nf-core/eager] error: Files could not be found. Do the specified FASTQ read files end in: '.fastq.gz', '.fq.gz', '.fastq', or '.fq'? Did you forget --single_end?" } .map { row -> [ row[0], [ row[1][0], row[1][1] ] ] } .ifEmpty { exit 1, "[nf-core/eager] error: --input was empty - no input files supplied!" } .into { ch_reads_for_faketsv; ch_reads_for_validate } diff --git a/nextflow.config b/nextflow.config index 956283e1c..ea64e9be7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -207,7 +207,6 @@ params { maltextract_megansummary = false maltextract_percentidentity = 85.0 maltextract_topalignment = false - maltextract_singlestranded = false // Boilerplate options name = false