diff --git a/conf/igenomes.config b/conf/igenomes.config
index 362d3625090d752449c0abc710ecaf1d0b4508f0..61de40b1236b8be39ac009ff54f46d99ceebeab6 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -12,152 +12,152 @@ params {
// illumina iGenomes reference file paths
genomes {
'GRCh37' {
- fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
}
'GRCh38' {
- fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
}
'GRCm38' {
- fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
}
'TAIR10' {
- fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
}
'EB2' {
- fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
}
'UMD3.1' {
- fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
}
'WBcel235' {
- fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
}
'CanFam3.1' {
- fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
}
'GRCz10' {
fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
+ bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
}
'BDGP6' {
- fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
}
'EquCab2' {
- fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
}
'EB1' {
- fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
}
'Galgal4' {
- fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
}
'Gm01' {
- fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
}
'Mmul_1' {
- fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
}
'IRGSP-1.0' {
- fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
}
'CHIMP2.1.4' {
- fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
}
'Rnor_6.0' {
- fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
}
'R64-1-1' {
- fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
}
'EF2' {
- fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
}
'Sbi1' {
- fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
}
'Sscrofa10.2' {
- fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
}
'AGPv3' {
- fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
}
'hg38' {
- fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
}
'hg19' {
- fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
}
'mm10' {
- fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
}
'bosTau8' {
- fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
}
'ce10' {
- fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
}
'canFam3' {
- fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
}
'danRer10' {
- fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
}
'dm6' {
- fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
}
'equCab2' {
- fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
}
'galGal4' {
- fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
}
'panTro4' {
- fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
}
'rn6' {
- fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
}
'sacCer3' {
- fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
}
'susScr3' {
- fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
}
}
}
diff --git a/conf/modules.config b/conf/modules.config
index f0311f6a918c284f844e531e4762884d4ef61338..32a65a438d07250e8db5020805b34197cbbb1cfc 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -46,8 +46,8 @@ process {
withName: 'BOWTIE2_ALIGN' {
publishDir = [
path: { "${params.outdir}/hicpro/mapping" },
- mode: 'copy',
- enabled: params.save_aligned_intermediates
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
]
ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
ext.args = params.bwt2_opts_end2end ?: ''
@@ -57,16 +57,16 @@ process {
withName: 'TRIM_READS' {
publishDir = [
path: { "${params.outdir}/hicpro/mapping/" },
- mode: 'copy',
- enabled: params.save_aligned_intermediates
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
]
}
withName: 'BOWTIE2_ALIGN_TRIMMED' {
publishDir = [
path: { "${params.outdir}/hicpro/mapping" },
- mode: 'copy',
- enabled: params.save_aligned_intermediates
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
]
ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}_trimmed" : "${meta.id}_${meta.mates}_trimmed" }
ext.args = params.bwt2_opts_trimmed ?: ''
@@ -76,8 +76,8 @@ process {
withName: 'MERGE_BOWTIE2' {
publishDir = [
path: { "${params.outdir}/hicpro/mapping" },
- mode: 'copy',
- enabled: params.save_aligned_intermediates
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
]
ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
}
@@ -85,13 +85,13 @@ process {
withName: 'COMBINE_MATES' {
publishDir = [
path: { "${params.outdir}/hicpro/mapping" },
- mode: 'copy',
- pattern: '*.bam'
+ mode: 'copy',
+ pattern: '*.bam'
]
ext.args = [
"-t",
- params.keep_multi ? "--multi" : "",
- params.min_mapq ? "-q ${params.min_mapq}" : ""
+ params.keep_multi ? "--multi" : "",
+ params.min_mapq ? "-q ${params.min_mapq}" : ""
].join(' ').trim()
ext.prefix = { params.split_fastq ? "${meta.chunk}" : "${meta.id}" }
}
@@ -99,26 +99,26 @@ process {
withName: 'GET_VALID_INTERACTION' {
publishDir = [
path: { "${params.outdir}/hicpro/valid_pairs" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename},
- mode: 'copy',
- enabled: params.save_pairs_intermediates
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename},
+ mode: 'copy',
+ enabled: params.save_pairs_intermediates
]
ext.args = { [
params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : '',
- params.min_insert_size > 0 ? " -s ${params.min_insert_size}" : '',
- params.max_insert_size > 0 ? " -l ${params.max_insert_size}" : '',
- params.min_restriction_fragment_size > 0 ? " -t ${params.min_restriction_fragment_size}" : '',
- params.max_restriction_fragment_size > 0 ? " -m ${params.max_restriction_fragment_size}" : '',
- params.save_interaction_bam ? " --sam" : ''
+ params.min_insert_size > 0 ? " -s ${params.min_insert_size}" : '',
+ params.max_insert_size > 0 ? " -l ${params.max_insert_size}" : '',
+ params.min_restriction_fragment_size > 0 ? " -t ${params.min_restriction_fragment_size}" : '',
+ params.max_restriction_fragment_size > 0 ? " -m ${params.max_restriction_fragment_size}" : '',
+ params.save_interaction_bam ? " --sam" : ''
].join(' ').trim() }
}
withName: 'GET_VALID_INTERACTION_DNASE' {
publishDir = [
path: { "${params.outdir}/hicpro/valid_pairs" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy',
- enabled: params.save_pairs_intermediates
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy',
+ enabled: params.save_pairs_intermediates
]
ext.args = { params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : "" }
}
@@ -127,13 +127,13 @@ process {
publishDir = [
[
path: { "${params.outdir}/hicpro/stats/${meta.id}" },
- mode: 'copy',
- pattern: "*stat"
+ mode: 'copy',
+ pattern: "*stat"
],
[
path: { "${params.outdir}/hicpro/valid_pairs" },
- mode: 'copy',
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy',
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*Pairs"
]
]
@@ -143,33 +143,33 @@ process {
withName: 'MERGE_STATS' {
publishDir = [
path: { "${params.outdir}/hicpro/stats/${meta.id}" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy',
- pattern: "*stat"
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy',
+ pattern: "*stat"
]
}
withName: 'HICPRO2PAIRS' {
publishDir = [
path: { "${params.outdir}/hicpro/valid_pairs/pairix/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
}
withName: 'BUILD_CONTACT_MAPS' {
publishDir = [
path: { "${params.outdir}/hicpro/matrix/raw" },
- mode: 'copy',
- enabled: params.hicpro_maps
+ mode: 'copy',
+ enabled: params.hicpro_maps
]
}
withName: 'ICE_NORMALIZATION' {
publishDir = [
path: { "${params.outdir}/hicpro/matrix/iced" },
- mode: 'copy',
- enabled: params.hicpro_maps
+ mode: 'copy',
+ enabled: params.hicpro_maps
]
}
@@ -179,8 +179,8 @@ process {
withName: 'HIC_PLOT_DIST_VS_COUNTS'{
publishDir = [
path: { "${params.outdir}/distance_decay/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
}
@@ -190,17 +190,17 @@ process {
withName: 'COOLER_MAKEBINS' {
publishDir = [
path: { "${params.outdir}/contact_maps/bins/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
}
withName: 'COOLER_CLOAD' {
publishDir = [
path: { "${params.outdir}/contact_maps/cool/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy',
- enabled : params.save_raw_maps
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy',
+ enabled : params.save_raw_maps
]
ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
}
@@ -208,8 +208,8 @@ process {
withName: 'COOLER_BALANCE' {
publishDir = [
path: { "${params.outdir}/contact_maps/cool/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
ext.args = '--force'
}
@@ -226,8 +226,8 @@ process {
publishDir = [
[
path: { "${params.outdir}/contact_maps/txt/" },
- mode: 'copy',
- pattern: "*_raw.txt",
+ mode: 'copy',
+ pattern: "*_raw.txt",
enabled: params.save_raw_maps
],
[
@@ -241,8 +241,8 @@ process {
withName: 'COOLER_ZOOMIFY' {
publishDir = [
path: { "${params.outdir}/contact_maps/cool/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
ext.args = "--balance"
}
@@ -253,8 +253,8 @@ process {
withName: 'CALL_COMPARTMENTS' {
publishDir = [
path: { "${params.outdir}/compartments/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
ext.args = '--bigwig'
}
@@ -265,8 +265,8 @@ process {
withName: 'INSULATION' {
publishDir = [
path: { "${params.outdir}/tads/insulation/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
ext.args = '15 25 50 --window-pixels'
}
@@ -274,8 +274,8 @@ process {
withName: 'HIC_FIND_TADS' {
publishDir = [
path: { "${params.outdir}/tads/hicExplorer" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
]
ext.args = '--correctForMultipleTesting fdr'
}