From f9d85ac006a2c7392458ae68fe3a92569d72f5a2 Mon Sep 17 00:00:00 2001 From: Flip Mulder <47565214+ffmmulder@users.noreply.github.com> Date: Sun, 4 Jul 2021 09:23:16 +0200 Subject: [PATCH] Delete UMCU_hg19_SE.config --- confs/UMCU_hg19_SE.config | 437 -------------------------------------- 1 file changed, 437 deletions(-) delete mode 100755 confs/UMCU_hg19_SE.config diff --git a/confs/UMCU_hg19_SE.config b/confs/UMCU_hg19_SE.config deleted file mode 100755 index c0375f3..0000000 --- a/confs/UMCU_hg19_SE.config +++ /dev/null @@ -1,437 +0,0 @@ - manifest { - homePage = 'https://github.com/UMCUGenetics/RNASeq-NF' - description = 'RNASeq-NF is an NGS analysis pipeline for RNA expression quantification' - mainScript = 'main.nf' - version = '1.0.4' - nextflowVersion = '20.04.1' -} - -params { - - /*==========================ƒ - Reference settings - /*==========================*/ - genome_fasta = '/hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fa' - genome_gtf = '/hpc/cog_bioinf/GENOMES/STAR/Homo_sapiens.GRCh37/Homo_sapiens.GRCh37.74.gtf' - genome_bed = '/hpc/cog_bioinf/ubec/tools/RSeQC/Homo_sapiens.GRCh37.74.bed12' - genome_dict = '/hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.dict' - genome_index = '/hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fa.fai' - genome_known_sites = ['/hpc/cog_bioinf/common_dbs/GATK_bundle/1000G_phase1.indels.b37.vcf', - '/hpc/cog_bioinf/common_dbs/GATK_bundle/dbsnp_137.b37.vcf', - '/hpc/cog_bioinf/common_dbs/GATK_bundle/Mills_and_1000G_gold_standard.indels.b37.vcf'] - scatter_interval_list = '/hpc/cog_bioinf/ubec/tools/Homo_sapiens.GRCh37.GATK.illumina.chromosomes.interval_list' - star_index = '/hpc/cog_bioinf/GENOMES/STAR/2.7.3a/Homo_sapiens.GRCh37.GATK.illumina' - salmon_index = '/hpc/cog_bioinf/GENOMES/Salmon/1.2.1/Homo_sapiens.GRCh37.75.cdna.all' - transcripts_fasta = '/hpc/cog_bioinf/GENOMES/RSEM/GRCh37/GRCh37.transcripts.fa' - - - /*==========================ƒ - workflow steps - /*==========================*/ - - // Pre-alignment processing. - runTrimGalore = true - runSortMeRNA = true - - // Alignment - STAR - Sambamba markdup - runMapping = true - - // Counting - SubRead / FeatureCounts - runFeatureCounts = true - - // Salmon - runSalmon = false - - // QC - runFastQC = true - runMultiQC = true - runPostQC = true - runRSeQC_TIN = true - - // GATK (v4) - runGermlineCallingGATK = false - runGATK4_BQSR = true - /*========================== - Settings - /*==========================*/ - - // Standard options - gencode = false - singleEnd = true - MergeFQ = true - help= false - customQC = true - - // CustomQC template - rmd_template = "$baseDir/bin/RNASeqNF_QC.Rmd" - - // Standard references - rRNA_database_manifest = "$baseDir/assets/sortmerna-db-default.txt" - - // Library strandedness - stranded = true - revstranded = false - unstranded = false - - // Custom settings of tools. - options.FastQC = '' - options.TrimGalore = '--fastqc' - options.SortMeRNA = '' - options.STAR = '--outReadsUnmapped Fastx' - options.FeatureCounts = '' - options.Salmon_quant = '--seqBias --useVBOpt --gcBias' - options.Salmon_index = '' - options.Salmon_quantmerge = '' - options.GATK4_SplitIntervals = '-SCATTER_COUNT 100 --UNIQUE true -M BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW' - options.GATK4_HaplotypeCaller = '--standard-min-confidence-threshold-for-calling 20.0 --dont-use-soft-clipped-bases' - options.GATK4_VariantFiltration = '--cluster-window-size 35 --cluster-size 3' - options.GATK4_BQRS = '' - options.Sambamba_MergeBams = '' - options.Preseq = "-v -B -D" - options.MultiQC = '' - - //featureCounts - fc_group_features = 'gene_id' - fc_count_type = 'exon' - fc_group_features_type = 'gene_biotype' - fc_extra_attributes = 'gene_name' - normalize_counts = true - biotypeQC = true - - // Salmon additional options - saveUnaligned = false - - //Memory settings for SGE profile - sambambamarkdup.mem = '32G' - splitintervals.mem = '12G' - baserecalibrator.mem = '9G' - gatherbaserecalibrator.mem = '6G' - applybqsr.mem = '9G' - haplotypecaller.mem = '25G' - mergevcf.mem = '14G' - variantfiltration.mem = '10G' - mergebams.mem = '5G' - multiqc.mem = '4G' - -} - -process { - errorStrategy = 'retry' - maxRetries = 1 - withLabel : STAR_2_7_3a_AlignReads { - time = '24h' - penv = 'threaded' - cpus = 4 - memory = '35G' - publishDir.path = "${params.out_dir}/STAR" - publishDir.mode = 'copy' - publishDir.saveAs = {filename -> if (filename.indexOf("_Log.out") > 0) "logs/$filename" - else if (filename.indexOf("_Log.final.out") > 0) "logs/$filename" - else if (filename.indexOf(".bam") > 0) "mapped/$filename" - else if (filename.indexOf("_SJ.out.tab") > 0) "SJ/$filename" - else if (filename.indexOf(".mate1") > 0) "unmapped/$filename" - else if (filename.indexOf(".mate2") > 0) "unmapped/$filename" } - - } - withLabel : Sambamba_0_7_0_Index { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '10G' - publishDir.path = "${params.out_dir}/STAR" - publishDir.mode = 'copy' - publishDir.saveAs = {filename -> if (filename.indexOf(".bai") > 0) "mapped/$filename" } - } - withLabel : Sambamba_0_7_0_Flagstat { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '5G' - publishDir.path = "${params.out_dir}/Sambamba/Flagstats" - publishDir.mode = 'copy' - - } - withLabel: RSeQC_3_0_1 { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '25G' - publishDir.path = "${params.out_dir}/QC/RSeQC" - publishDir.mode = 'copy' - publishDir.saveAs = {filename -> - if (filename.indexOf("bam_stat.txt") > 0) "bam_stat/$filename" - else if (filename.indexOf("infer_experiment.txt") > 0) "infer_experiment/$filename" - else if (filename.indexOf("read_distribution.txt") > 0) "read_distribution/$filename" - else if (filename.indexOf("read_duplication.DupRate_plot.pdf") > 0) "read_duplication/$filename" - else if (filename.indexOf("read_duplication.DupRate_plot.r") > 0) "read_duplication/rscripts/$filename" - else if (filename.indexOf("read_duplication.pos.DupRate.xls") > 0) "read_duplication/dup_pos/$filename" - else if (filename.indexOf("read_duplication.seq.DupRate.xls") > 0) "read_duplication/dup_seq/$filename" - else if (filename.indexOf("RPKM_saturation.eRPKM.xls") > 0) "RPKM_saturation/rpkm/$filename" - else if (filename.indexOf("RPKM_saturation.rawCount.xls") > 0) "RPKM_saturation/counts/$filename" - else if (filename.indexOf("RPKM_saturation.saturation.pdf") > 0) "RPKM_saturation/$filename" - else if (filename.indexOf("RPKM_saturation.saturation.r") > 0) "RPKM_saturation/rscripts/$filename" - else if (filename.indexOf("inner_distance.txt") > 0) "inner_distance/$filename" - else if (filename.indexOf("inner_distance_freq.txt") > 0) "inner_distance/data/$filename" - else if (filename.indexOf("inner_distance_plot.r") > 0) "inner_distance/rscripts/$filename" - else if (filename.indexOf("inner_distance_plot.pdf") > 0) "inner_distance/plots/$filename" - else if (filename.indexOf("junction_plot.r") > 0) "junction_annotation/rscripts/$filename" - else if (filename.indexOf("junction.xls") > 0) "junction_annotation/data/$filename" - else if (filename.indexOf(".junction_annotation_log.txt") > 0) "junction_annotation/log/$filename" - else if (filename.indexOf("splice_events.pdf") > 0) "junction_annotation/events/$filename" - else if (filename.indexOf("splice_junction.pdf") > 0) "junction_annotation/junctions/$filename" - else if (filename.indexOf("junctionSaturation_plot.pdf") > 0) "junction_saturation/$filename" - else if (filename.indexOf("junctionSaturation_plot.r") > 0) "junction_saturation/rscripts/$filename" - else filename } - } - withLabel: RSeQC_3_0_1_TIN { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '35G' - publishDir.path = "${params.out_dir}/QC/RSeQC/TIN" - publishDir.mode = 'copy' - } - withLabel: Preseq_2_0_3 { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '15G' - publishDir.path = "${params.out_dir}/QC/Preseq" - publishDir.mode = 'copy' - publishDir.saveAs = {filename -> if (filename.indexOf(".ccurve.txt") > 0) "complexity_curve/$filename" } - } - withLabel : Sambamba_0_7_0_Markdup { - time = '24h' - penv = 'threaded' - cpus = 6 - memory = '32G' - //publishDir.path = "${params.out_dir}/Sambamba/Markdup" - //publishDir.mode = 'copy' - } - withLabel : GATK_4_1_3_0_SplitNCigarReads { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '12G' - //publishDir.path = "${params.out_dir}/GATK/bam" - } - withLabel : Salmon_1_2_1_Quant { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '25G' - publishDir.path = "${params.out_dir}/Salmon" - publishDir.mode = 'copy' - } - withLabel : Salmon_1_2_1_QuantMerge { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '5G' - publishDir.path = "${params.out_dir}/Salmon/merged" - publishDir.mode = 'copy' - } - withLabel : Salmon_1_2_1_Index { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '25G' - publishDir.path = "${params.out_dir}/reference_resources/Salmon" - publishDir.mode = 'copy' - } - withLabel: GATK_4_1_3_0_SplitIntervals { - memory = '12G' - time = '1h' - } - withLabel : GATK_4_1_3_0_BaseRecalibration { - memory = '9G' - time = '1h' - } - withLabel : GATK_4_1_3_0_GatherBaseRecalibrationTables { - memory = '6G' - time = '1h' - } - withLabel : GATK_4_1_3_0_BaseRecalibrationTable { - memory = '9G' - time = '1h' - } - withLabel : GATK_4_1_3_0_HaplotypeCaller { - memory = '25G' - time = '12h' - } - withLabel : GATK_4_1_3_0_MergeVCFs { - memory = '14G' - time = '4h' - publishDir.path = "${params.out_dir}/GATK/vcf/raw" - publishDir.mode = 'copy' - } - withLabel : GATK_4_1_3_0_VariantFiltration { - memory = '10G' - time = '4h' - publishDir.path = "${params.out_dir}/GATK/vcf/filtered" - publishDir.mode = 'copy' - } - withLabel : Sambamba_0_7_0_Merge { - cpus = 10 - penv = 'threaded' - memory = '5G' - time = '2h' - //publishDir.path = "${params.out_dir}/GATK/bam" - } - withLabel : MultiQC_1_9 { - memory = '4G' - time = '1h' - publishDir.path = "${params.out_dir}/report/MultiQC" - publishDir.mode = 'copy' - } - withLabel : rnaseqnfqc_1_0_0 { - memory = '4G' - time = '1h' - publishDir.path = "${params.out_dir}/report/Custom_QC" - publishDir.mode = 'copy' - } - withLabel : biconductor_3_20_7_edger_normalize { - memory = '5G' - time = '1h' - publishDir.path = "${params.out_dir}/featureCounts" - publishDir.mode = 'copy' - } - withLabel : biconductor_1_28_0_deseq2normalize { - memory = '5G' - time = '1h' - publishDir.path = "${params.out_dir}/featureCounts" - publishDir.mode = 'copy' - - } - withLabel : Subread_2_0_0_FeatureCounts { - time = '24h' - penv = 'threaded' - cpus = 10 - memory = '25G' - publishDir.path = "${params.out_dir}/featureCounts" - publishDir.mode = 'copy' - publishDir.saveAs = {filename -> if (filename.indexOf("_biotype_") > 0) "biotypes/$filename" - else filename } - - } - withLabel : STAR_2_7_3a_GenomeGenerate { - time = '24h' - penv = 'threaded' - cpus = 12 - memory = '150G' - publishDir.path = "${params.out_dir}/reference_resources/STAR" - publishDir.mode = 'copy' - } - withLabel : ucsc_377_GenePredToBed { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '15G' - publishDir.path = "${params.out_dir}/reference_resources" - publishDir.mode = 'copy' - } - withLabel : ucsc_377_GtfToGenePred { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '15G' - } - withLabel : CreateIntervalList { - time = '1h' - publishDir.path = "${params.out_dir}/reference_resources" - publishDir.mode = 'copy' - } - withLabel : FASTQC_0_11_8 { - time = '1h' - publishDir.path = "${params.out_dir}/QC/FastQC/raw" - publishDir.mode = 'copy' - } - withLabel : SortMeRNA_4_2_0 { - time = '24h' - penv = 'threaded' - cpus = 4 - memory = '15G' - publishDir.path = "${params.out_dir}/QC/" - publishDir.mode = 'copy' - publishDir.saveAs = {filename -> - if (filename.indexOf("_rRNA_report.txt") > 0) "SorteMeRNA/logs/$filename" - else if (filename.indexOf("_filtered_rRNA.fastq.gz") > 0) "SorteMeRNA/rRNA-reads/$filename" - else null } - - } - withLabel : TrimGalore_0_6_5 { - time = '24h' - penv = 'threaded' - cpus = 2 - memory = '6G' - publishDir.path = "${params.out_dir}/QC/TrimGalore" - publishDir.mode = 'copy' - publishDir.saveAs = {filename -> - if (filename.indexOf("_fastqc") > 0) "FastQC/$filename" - else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename" - else null } - } -} - -executor { - $sge { - queueSize = 1000 - pollInterval = '30sec' - queueStatInterval = '5min' - } - $slurm { - queueSize = 1000 - pollInterval = '30sec' - queueStatInterval = '5min' - } -} - -profiles { - sge { - process.executor = 'sge' - process.queue = 'all.q' - process.clusterOptions = '-P compgen ' - } - - slurm { - process.executor = 'slurm' - process.clusterOptions = '--gres=tmpspace:25G' - process.queue = 'cpu' - } -} - -report { - enabled = true - file = "$params.out_dir/log/nextflow_report.html" -} - -trace { - enabled = true - file = "$params.out_dir/log/nextflow_trace.txt" - fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt' -} - -timeline { - enabled = true - file = "$params.out_dir/log/nextflow_timeline.html" -} - -singularity { - enabled = true - autoMounts = true - runOptions = '-B /hpc -B $TMPDIR:$TMPDIR' - cacheDir = '/hpc/local/CentOS7/cog_bioinf/singularity_cache' -} - -cleanup = true - - - - - - - - - - -