From 806a6451c3e92cdfdc98fb7bbc5991bc5511bdd8 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 25 Feb 2019 15:37:19 +0000 Subject: [PATCH] Split paths to obtain bwa_index parameters --- conf/igenomes.config | 52 ++++++++++++++++++++++---------------------- docs/usage.md | 15 ++++--------- main.nf | 49 ++++++++++++++++++++++------------------- nextflow.config | 2 -- 4 files changed, 57 insertions(+), 61 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 65ffaaf9..e8c591fa 100755 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -12,7 +12,7 @@ params { genomes { 'GRCh37' { fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" blacklist = "${baseDir}/assets/blacklists/GRCh37-blacklist.bed" macs_gsize = "2.7e9" @@ -20,7 +20,7 @@ params { } 'GRCh38' { fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" blacklist = "${baseDir}/assets/blacklists/hg38-blacklist.bed" macs_gsize = "2.7e9" @@ -28,7 +28,7 @@ params { } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" blacklist = "${baseDir}/assets/blacklists/GRCm38-blacklist.bed" macs_gsize = "1.87e9" @@ -36,127 +36,127 @@ params { } 'TAIR10' { fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" mito_name = "Mt" } 'EB2' { fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" } 'UMD3.1' { fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" mito_name = "MT" } 'WBcel235' { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" macs_gsize = "9e7" mito_name = "MtDNA" } 'CanFam3.1' { fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" mito_name = "MT" } 'GRCz10' { fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" mito_name = "MT" } 'BDGP6' { fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" macs_gsize = "1.2e8" mito_name = "M" } 'EquCab2' { fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" mito_name = "MT" } 'EB1' { fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" } 'Galgal4' { fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" mito_name = "MT" } 'Gm01' { fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" } 'Mmul_1' { fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" mito_name = "MT" } 'IRGSP-1.0' { fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" mito_name = "Mt" } 'CHIMP2.1.4' { fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" mito_name = "MT" } 'Rnor_6.0' { fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" mito_name = "MT" } 'R64-1-1' { fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" macs_gsize = "1.2e7" mito_name = "MT" } 'EF2' { fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" macs_gsize = "1.21e7" mito_name = "MT" } 'Sbi1' { fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" } 'Sscrofa10.2' { fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" mito_name = "MT" } 'AGPv3' { fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" mito_name = "Mt" } 'hg38' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" blacklist = "${baseDir}/assets/blacklists/hg38-blacklist.bed" macs_gsize = "2.7e9" @@ -164,7 +164,7 @@ params { } 'hg19' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" blacklist = "${baseDir}/assets/blacklists/hg19-blacklist.bed" macs_gsize = "2.7e9" @@ -172,7 +172,7 @@ params { } 'mm10' { fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/" + bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa" gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" blacklist = "${baseDir}/assets/blacklists/mm10-blacklist.bed" macs_gsize = "1.87e9" diff --git a/docs/usage.md b/docs/usage.md index 257885b9..90f4ed7a 100755 --- a/docs/usage.md +++ b/docs/usage.md @@ -22,8 +22,7 @@ * [`--genome`](#--genome) * [`--fasta`](#--fasta) * [`--gtf`](#--gtf) - * [`--bwa_index_dir`](#--bwa_index_dir) - * [`--bwa_index_base`](#--bwa_index_base) + * [`--bwa_index`](#--bwa_index) * [`--gene_bed`](#--gene_bed) * [`--tss_bed`](#--tss_bed) * [`--mito_name`](#--mito_name) @@ -237,16 +236,10 @@ The full path to GTF file for annotating peaks (*mandatory* if `--genome` is not --gtf '[path to GTF file]' ``` -### `--bwa_index_dir` -Directory containing an existing BWA index for your reference genome. +### `--bwa_index` +Full path to an existing BWA index for your reference genome including the base name for the index. ```bash ---bwa_index_dir '[directory containing BWA index]' -``` - -### `--bwa_index_base` -Base file name for an existing BWA index for your reference genome. Default: `genome.fa`. -```bash ---bwa_index_base '[basename of BWA index]' +--bwa_index '[directory containing BWA index]/genome.fa' ``` ### `--gene_bed` diff --git a/main.nf b/main.nf index 8a2f9ad1..35a6fdae 100755 --- a/main.nf +++ b/main.nf @@ -40,8 +40,7 @@ def helpMessage() { --fragment_size [int] Estimated fragment size used to extend single-end reads. Default: 0 References If not specified in the configuration file or you wish to overwrite any of the references - --bwa_index_dir Directory containing BWA index - --bwa_index_base Basename for BWA index. Default: genome.fa + --bwa_index Full path to directory containing BWA index including base name i.e. /path/to/index/genome.fa --gene_bed Path to BED file containing gene intervals --tss_bed Path to BED file containing transcription start sites (used by ataqv) --mito_name Name of Mitochondrial chomosome in genome fasta (e.g. chrM). Reads aligning to this contig are filtered out @@ -105,7 +104,7 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome // Configurable variables params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false -params.bwa_index_dir = params.genome ? params.genomes[ params.genome ].bwa ?: false : false +params.bwa_index = params.genome ? params.genomes[ params.genome ].bwa ?: false : false params.gtf = params.genome ? params.genomes[ params.genome ].gtf ?: false : false params.gene_bed = params.genome ? params.genomes[ params.genome ].gene_bed ?: false : false params.mito_name = params.genome ? params.genomes[ params.genome ].mito_name ?: false : false @@ -161,6 +160,9 @@ if (params.design){ } if (params.fasta){ + lastPath = params.fasta.lastIndexOf(File.separator) + bwa_base = params.fasta.substring(lastPath+1) + Channel .fromPath(params.fasta, checkIfExists: true) .ifEmpty { exit 1, "Fasta file not found: ${params.fasta}" } @@ -190,10 +192,14 @@ if (params.gtf){ exit 1, "GTF annotation file not specified!" } -if (params.bwa_index_dir){ +if (params.bwa_index){ + lastPath = params.bwa_index.lastIndexOf(File.separator) + bwa_dir = params.bwa_index.substring(0,lastPath+1) + bwa_base = params.bwa_index.substring(lastPath+1) + bwa_index = Channel - .fromPath(params.bwa_index_dir, checkIfExists: true) - .ifEmpty { exit 1, "BWA index not found: ${params.bwa_index_dir}" } + .fromPath(bwa_dir, checkIfExists: true) + .ifEmpty { exit 1, "BWA index directory not found: ${bwa_dir}" } } if (params.gene_bed){ @@ -244,18 +250,17 @@ def summary = [:] summary['Pipeline Name'] = 'nf-core/atacseq' summary['Pipeline Version'] = workflow.manifest.version summary['Run Name'] = custom_runName ?: workflow.runName -summary['Genome'] = params.genome ? params.genome : 'Not supplied' +summary['Genome'] = params.genome ?: 'Not supplied' summary['Data Type'] = params.singleEnd ? 'Single-End' : 'Paired-End' summary['Design File'] = params.design -if (params.bwa_index_dir) summary['BWA Index Directory'] = params.bwa_index_dir ? params.bwa_index_dir : 'Not supplied' -if (params.bwa_index_dir) summary['BWA Index Base'] = params.bwa_index_base ? params.bwa_index_base : 'Not supplied' +if (params.bwa_index) summary['BWA Index'] = params.bwa_index ?: 'Not supplied' summary['Fasta Ref'] = params.fasta summary['GTF File'] = params.gtf -summary['Gene BED File'] = params.gene_bed ? params.gene_bed : 'Not supplied' -summary['TSS BED File'] = params.tss_bed ? params.tss_bed : 'Not supplied' +summary['Gene BED File'] = params.gene_bed ?: 'Not supplied' +summary['TSS BED File'] = params.tss_bed ?: 'Not supplied' if (params.blacklist) summary['Blacklist BED'] = params.blacklist -summary['Mitochondrial Contig'] = params.mito_name ? params.mito_name : 'Not supplied' -summary['MACS Genome Size'] = params.macs_gsize ? params.macs_gsize : 'Not supplied' +summary['Mitochondrial Contig'] = params.mito_name ?: 'Not supplied' +summary['MACS Genome Size'] = params.macs_gsize ?: 'Not supplied' if (params.macs_gsize) summary['MACS Narrow Peaks'] = params.narrowPeak ? 'Yes' : 'No' if (params.skipTrimming){ summary['Trimming Step'] = 'Skipped' @@ -377,7 +382,7 @@ multiple_samples = design_multiple_samples.map { it -> it[0][0..-7] } /* * PREPROCESSING - Build BWA index */ -if (!params.bwa_index_dir){ +if (!params.bwa_index){ process makeBWAindex { tag "$fasta" label 'process_big' @@ -592,7 +597,7 @@ process bwa_mem { prefix="${name}.Lb" rg="\'@RG\\tID:${name}\\tSM:${name.toString().subSequence(0, name.length() - 3)}\\tPL:ILLUMINA\\tLB:${name}\\tPU:1\'" """ - bwa mem -t $task.cpus -M -R $rg ${index}/${params.bwa_index_base} $reads | samtools view -@ $task.cpus -b -h -F 0x0100 -O BAM -o ${prefix}.bam - + bwa mem -t $task.cpus -M -R $rg ${index}/${bwa_base} $reads | samtools view -@ $task.cpus -b -h -F 0x0100 -O BAM -o ${prefix}.bam - """ } @@ -742,7 +747,7 @@ process merge_library_filter { output: set val(name), file("*.{bam,bam.bai}") into mlib_filter_bam - file "*.flagstat" into mlib_filter_flagstat + set val(name), file("*.flagstat") into mlib_filter_flagstat file "*.{idxstats,stats}" into mlib_filter_stats_mqc script: @@ -775,7 +780,8 @@ process merge_library_filter { * STEP 4.3 Remove orphan reads from paired-end BAM file */ if (params.singleEnd){ - mlib_filter_bam.into { mlib_rm_orphan_bam_bigwig; + mlib_filter_bam.into { mlib_rm_orphan_bam_metrics; + mlib_rm_orphan_bam_bigwig; mlib_rm_orphan_bam_macs; mlib_rm_orphan_bam_mrep; mlib_name_bam_mlib_counts; @@ -783,8 +789,7 @@ if (params.singleEnd){ mlib_filter_flagstat.into { mlib_rm_orphan_flagstat_bigwig; mlib_rm_orphan_flagstat_macs; mlib_rm_orphan_flagstat_mqc } - mlib_filter_stats_mqc.into { mlib_rm_orphan_stats_mqc } - + mlib_filter_stats_mqc.set { mlib_rm_orphan_stats_mqc } } else { process merge_library_rm_orphan { tag "$name" @@ -809,9 +814,9 @@ if (params.singleEnd){ mlib_rm_orphan_bam_mrep set val(name), file("${prefix}.bam") into mlib_name_bam_mlib_counts, mlib_name_bam_mrep_counts - set val(name), "*.flagstat" into mlib_rm_orphan_flagstat_bigwig, - mlib_rm_orphan_flagstat_macs, - mlib_rm_orphan_flagstat_mqc + set val(name), file("*.flagstat") into mlib_rm_orphan_flagstat_bigwig, + mlib_rm_orphan_flagstat_macs, + mlib_rm_orphan_flagstat_mqc file "*.{idxstats,stats}" into mlib_rm_orphan_stats_mqc script: // This script is bundled with the pipeline, in nf-core/atacseq/bin/ diff --git a/nextflow.config b/nextflow.config index ef481765..08baa4cf 100755 --- a/nextflow.config +++ b/nextflow.config @@ -20,7 +20,6 @@ params { fragment_size = 0 // Options: References - bwa_index_base = 'genome.fa' tss_bed = false saveGenomeIndex = false @@ -85,7 +84,6 @@ profiles { } singularity { singularity.enabled = true - process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"} } test { includeConfig 'conf/test.config' } }