diff --git a/bin/src/cutsite_trimming.cpp b/bin/src/cutsite_trimming.cpp
index d8ab26f1f522723bf34a8e16ee9cba19f7780da1..03cb20f3f74ff0282ad6560f029d0a9975fe517b 100644
--- a/bin/src/cutsite_trimming.cpp
+++ b/bin/src/cutsite_trimming.cpp
@@ -29,33 +29,33 @@ static int get_options(int argc, char* argv[], std::string& fastqFile,
exit(usage());
}
for (int ac = 1; ac < argc; ++ac) {
- const char* opt = argv[ac];
- if (*opt == '-') {
- if (!strcmp(opt, "--fastq")) {
- fastqFile = std::string(argv[++ac]);
- }
- else if (!strcmp(opt, "--cutsite")) {
- std::string cutSitesSequence;
- cutSitesSequence = std::string(argv[++ac]);
- size_t pos = cutSitesSequence.find(",");
- size_t begin = 0;
- while(pos != std::string::npos){
- cutSites.push_back(cutSitesSequence.substr(begin, pos - begin));
- begin = pos + 1;
- pos = cutSitesSequence.find(",", begin + 1);
- }
- cutSites.push_back(cutSitesSequence.substr(begin, pos));
- }
- else if (!strcmp(opt, "--out")) {
- output = std::string(argv[++ac]);
- }
- else if (!strcmp(opt, "--rmuntrim")) {
- rmuntrim = true;
- }
- }else {
- std::cerr << prog << ": unknown option " << opt << std::endl;
- return usage();
- }
+ const char* opt = argv[ac];
+ if (*opt == '-') {
+ if (!strcmp(opt, "--fastq")) {
+ fastqFile = std::string(argv[++ac]);
+ }
+ else if (!strcmp(opt, "--cutsite")) {
+ std::string cutSitesSequence;
+ cutSitesSequence = std::string(argv[++ac]);
+ size_t pos = cutSitesSequence.find(",");
+ size_t begin = 0;
+ while(pos != std::string::npos){
+ cutSites.push_back(cutSitesSequence.substr(begin, pos - begin));
+ begin = pos + 1;
+ pos = cutSitesSequence.find(",", begin + 1);
+ }
+ cutSites.push_back(cutSitesSequence.substr(begin, pos));
+ }
+ else if (!strcmp(opt, "--out")) {
+ output = std::string(argv[++ac]);
+ }
+ else if (!strcmp(opt, "--rmuntrim")) {
+ rmuntrim = true;
+ }
+ }else {
+ std::cerr << prog << ": unknown option " << opt << std::endl;
+ return usage();
+ }
}
return 0;
}
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 99ae9dba917fd600df00efa6c4760b3e876ae73f..362d3625090d752449c0abc710ecaf1d0b4508f0 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -9,155 +9,155 @@
*/
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/"
+ // 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/"
+ }
+ 'GRCh38' {
+ 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/"
+ }
+ 'TAIR10' {
+ 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/"
+ }
+ '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/"
+ }
+ 'WBcel235' {
+ 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/"
+ }
+ 'GRCz10' {
+ fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${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/"
+ }
+ 'EquCab2' {
+ 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/"
+ }
+ 'Galgal4' {
+ 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/"
+ }
+ '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/"
+ }
+ '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/"
+ }
+ '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/"
+ }
+ '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/"
+ }
+ '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/"
+ }
+ 'EF2' {
+ 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/"
+ }
+ '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/"
+ }
+ 'AGPv3' {
+ 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/"
+ }
+ 'hg19' {
+ 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/"
+ }
+ 'bosTau8' {
+ 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/"
+ }
+ 'canFam3' {
+ 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/"
+ }
+ 'dm6' {
+ 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/"
+ }
+ 'galGal4' {
+ 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/"
+ }
+ 'rn6' {
+ 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/"
+ }
+ 'susScr3' {
+ fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/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/"
- }
- 'GRCm38' {
- 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/"
- }
- '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/"
- }
- '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/"
- }
- 'WBcel235' {
- 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/"
- }
- 'GRCz10' {
- fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${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/"
- }
- 'EquCab2' {
- 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/"
- }
- 'Galgal4' {
- 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/"
- }
- '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/"
- }
- '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/"
- }
- '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/"
- }
- '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/"
- }
- '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/"
- }
- 'EF2' {
- 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/"
- }
- '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/"
- }
- 'AGPv3' {
- 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/"
- }
- 'hg19' {
- 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/"
- }
- 'bosTau8' {
- 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/"
- }
- 'canFam3' {
- 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/"
- }
- 'dm6' {
- 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/"
- }
- 'galGal4' {
- 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/"
- }
- 'rn6' {
- 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/"
- }
- 'susScr3' {
- 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 44ec6706090b6bcb18a54105e247a896db3a190d..f0311f6a918c284f844e531e4762884d4ef61338 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -1,282 +1,282 @@
process {
- //Default
- publishDir = [
- path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
- mode: 'copy',
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
-
- withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
+ //Default
publishDir = [
- path: { "${params.outdir}/pipeline_info" },
- mode: 'copy',
- pattern: '*_versions.yml'
+ path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+ mode: 'copy',
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
- }
- //**********************************************
- // PREPARE_GENOME
- withName: 'BOWTIE2_BUILD' {
- publishDir = [
- path: { "${params.outdir}/genome/bowtie2" },
- mode: 'copy',
- enabled: params.save_reference
- ]
- }
+ withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
+ publishDir = [
+ path: { "${params.outdir}/pipeline_info" },
+ mode: 'copy',
+ pattern: '*_versions.yml'
+ ]
+ }
- withName: 'CUSTOM_GETCHROMSIZES' {
- publishDir = [
- path: { "${params.outdir}/genome" },
- mode: 'copy',
- enabled: params.save_reference
- ]
- }
+ //**********************************************
+ // PREPARE_GENOME
+ withName: 'BOWTIE2_BUILD' {
+ publishDir = [
+ path: { "${params.outdir}/genome/bowtie2" },
+ mode: 'copy',
+ enabled: params.save_reference
+ ]
+ }
- withName: 'GET_RESTRICTION_FRAGMENTS' {
- publishDir = [
- path: { "${params.outdir}/genome" },
- mode: 'copy',
- enabled: params.save_reference
- ]
- }
+ withName: 'CUSTOM_GETCHROMSIZES' {
+ publishDir = [
+ path: { "${params.outdir}/genome" },
+ mode: 'copy',
+ enabled: params.save_reference
+ ]
+ }
- //*******************************************
- // HICPRO
- withName: 'BOWTIE2_ALIGN' {
- publishDir = [
- path: { "${params.outdir}/hicpro/mapping" },
- 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 ?: ''
- ext.args2 = !params.dnase ? "-F 4" :""
- }
+ withName: 'GET_RESTRICTION_FRAGMENTS' {
+ publishDir = [
+ path: { "${params.outdir}/genome" },
+ mode: 'copy',
+ enabled: params.save_reference
+ ]
+ }
- withName: 'TRIM_READS' {
- publishDir = [
- path: { "${params.outdir}/hicpro/mapping/" },
- mode: 'copy',
- enabled: params.save_aligned_intermediates
- ]
- }
+ //*******************************************
+ // HICPRO
+ withName: 'BOWTIE2_ALIGN' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/mapping" },
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
+ ]
+ ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
+ ext.args = params.bwt2_opts_end2end ?: ''
+ ext.args2 = !params.dnase ? "-F 4" :""
+ }
- withName: 'BOWTIE2_ALIGN_TRIMMED' {
- publishDir = [
- path: { "${params.outdir}/hicpro/mapping" },
- 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 ?: ''
- ext.args2 = ""
- }
+ withName: 'TRIM_READS' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/mapping/" },
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
+ ]
+ }
- withName: 'MERGE_BOWTIE2' {
- publishDir = [
- path: { "${params.outdir}/hicpro/mapping" },
- mode: 'copy',
- enabled: params.save_aligned_intermediates
- ]
- ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
- }
+ withName: 'BOWTIE2_ALIGN_TRIMMED' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/mapping" },
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
+ ]
+ ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}_trimmed" : "${meta.id}_${meta.mates}_trimmed" }
+ ext.args = params.bwt2_opts_trimmed ?: ''
+ ext.args2 = ""
+ }
- withName: 'COMBINE_MATES' {
- publishDir = [
- path: { "${params.outdir}/hicpro/mapping" },
- mode: 'copy',
- pattern: '*.bam'
- ]
- ext.args = [
- "-t",
- params.keep_multi ? "--multi" : "",
- params.min_mapq ? "-q ${params.min_mapq}" : ""
- ].join(' ').trim()
- ext.prefix = { params.split_fastq ? "${meta.chunk}" : "${meta.id}" }
- }
+ withName: 'MERGE_BOWTIE2' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/mapping" },
+ mode: 'copy',
+ enabled: params.save_aligned_intermediates
+ ]
+ ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
+ }
- 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
- ]
- 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 ${params.max_restriction_fragment_size}" : '',
- params.save_interaction_bam ? " --sam" : ''
- ].join(' ').trim() }
- }
+ withName: 'COMBINE_MATES' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/mapping" },
+ mode: 'copy',
+ pattern: '*.bam'
+ ]
+ ext.args = [
+ "-t",
+ params.keep_multi ? "--multi" : "",
+ params.min_mapq ? "-q ${params.min_mapq}" : ""
+ ].join(' ').trim()
+ ext.prefix = { params.split_fastq ? "${meta.chunk}" : "${meta.id}" }
+ }
- withName: 'GET_VALID_INTERACTION_DNASE' {
- publishDir = [
- path: { "${params.outdir}/hicpro/valid_pairs" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy',
- enabled: params.save_pairs_intermediates
- ]
- ext.args = { params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : "" }
- }
+ withName: 'GET_VALID_INTERACTION' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/valid_pairs" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename},
+ mode: 'copy',
+ enabled: params.save_pairs_intermediates
+ ]
+ 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 ${params.max_restriction_fragment_size}" : '',
+ params.save_interaction_bam ? " --sam" : ''
+ ].join(' ').trim() }
+ }
- withName: 'MERGE_VALID_INTERACTION' {
- publishDir = [
- [
- path: { "${params.outdir}/hicpro/stats/${meta.id}" },
- mode: 'copy',
- pattern: "*stat"
- ],
- [
- path: { "${params.outdir}/hicpro/valid_pairs" },
- mode: 'copy',
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- pattern: "*Pairs"
- ]
- ]
- ext.args = { params.keep_dups ? '' : '-d' }
- }
+ 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
+ ]
+ ext.args = { params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : "" }
+ }
- withName: 'MERGE_STATS' {
- publishDir = [
- path: { "${params.outdir}/hicpro/stats/${meta.id}" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy',
- pattern: "*stat"
- ]
- }
+ withName: 'MERGE_VALID_INTERACTION' {
+ publishDir = [
+ [
+ path: { "${params.outdir}/hicpro/stats/${meta.id}" },
+ mode: 'copy',
+ pattern: "*stat"
+ ],
+ [
+ path: { "${params.outdir}/hicpro/valid_pairs" },
+ mode: 'copy',
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ pattern: "*Pairs"
+ ]
+ ]
+ ext.args = { params.keep_dups ? '' : '-d' }
+ }
- withName: 'HICPRO2PAIRS' {
- publishDir = [
- path: { "${params.outdir}/hicpro/valid_pairs/pairix/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- }
+ withName: 'MERGE_STATS' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/stats/${meta.id}" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy',
+ pattern: "*stat"
+ ]
+ }
- withName: 'BUILD_CONTACT_MAPS' {
- publishDir = [
- path: { "${params.outdir}/hicpro/matrix/raw" },
- mode: 'copy',
- enabled: params.hicpro_maps
- ]
- }
+ withName: 'HICPRO2PAIRS' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/valid_pairs/pairix/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ }
- withName: 'ICE_NORMALIZATION' {
- publishDir = [
- path: { "${params.outdir}/hicpro/matrix/iced" },
- mode: 'copy',
- enabled: params.hicpro_maps
- ]
- }
+ withName: 'BUILD_CONTACT_MAPS' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/matrix/raw" },
+ mode: 'copy',
+ enabled: params.hicpro_maps
+ ]
+ }
- //*****************************************
- // QUALITY METRICS
+ withName: 'ICE_NORMALIZATION' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/matrix/iced" },
+ mode: 'copy',
+ enabled: params.hicpro_maps
+ ]
+ }
- withName: 'HIC_PLOT_DIST_VS_COUNTS'{
- publishDir = [
- path: { "${params.outdir}/distance_decay/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- }
+ //*****************************************
+ // QUALITY METRICS
- //*****************************************
- // COOLER
+ withName: 'HIC_PLOT_DIST_VS_COUNTS'{
+ publishDir = [
+ path: { "${params.outdir}/distance_decay/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ }
- withName: 'COOLER_MAKEBINS' {
- publishDir = [
- path: { "${params.outdir}/contact_maps/bins/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- }
+ //*****************************************
+ // COOLER
- withName: 'COOLER_CLOAD' {
- publishDir = [
- path: { "${params.outdir}/contact_maps/cool/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy',
- enabled : params.save_raw_maps
- ]
- ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
- }
+ withName: 'COOLER_MAKEBINS' {
+ publishDir = [
+ path: { "${params.outdir}/contact_maps/bins/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ }
- withName: 'COOLER_BALANCE' {
- publishDir = [
- path: { "${params.outdir}/contact_maps/cool/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- ext.args = '--force'
- }
+ withName: 'COOLER_CLOAD' {
+ publishDir = [
+ path: { "${params.outdir}/contact_maps/cool/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy',
+ enabled : params.save_raw_maps
+ ]
+ ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
+ }
- withName: 'COOLER_DUMP' {
- publishDir = [
- enabled: false
- ]
- ext.prefix = { "${cool.baseName}" }
- ext.args = "--one-based-ids --balanced --na-rep 0"
- }
+ withName: 'COOLER_BALANCE' {
+ publishDir = [
+ path: { "${params.outdir}/contact_maps/cool/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ ext.args = '--force'
+ }
- withName:'SPLIT_COOLER_DUMP' {
- publishDir = [
- [
- path: { "${params.outdir}/contact_maps/txt/" },
- mode: 'copy',
- pattern: "*_raw.txt",
- enabled: params.save_raw_maps
- ],
- [
- path: { "${params.outdir}/contact_maps/txt/" },
- mode: 'copy',
- pattern: "*_balanced.txt"
- ]
- ]
- }
+ withName: 'COOLER_DUMP' {
+ publishDir = [
+ enabled: false
+ ]
+ ext.prefix = { "${cool.baseName}" }
+ ext.args = "--one-based-ids --balanced --na-rep 0"
+ }
- withName: 'COOLER_ZOOMIFY' {
- publishDir = [
- path: { "${params.outdir}/contact_maps/cool/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- ext.args = "--balance"
- }
+ withName:'SPLIT_COOLER_DUMP' {
+ publishDir = [
+ [
+ path: { "${params.outdir}/contact_maps/txt/" },
+ mode: 'copy',
+ pattern: "*_raw.txt",
+ enabled: params.save_raw_maps
+ ],
+ [
+ path: { "${params.outdir}/contact_maps/txt/" },
+ mode: 'copy',
+ pattern: "*_balanced.txt"
+ ]
+ ]
+ }
- //********************************
- // COMPARTMENTS
+ withName: 'COOLER_ZOOMIFY' {
+ publishDir = [
+ path: { "${params.outdir}/contact_maps/cool/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ ext.args = "--balance"
+ }
- withName: 'CALL_COMPARTMENTS' {
- publishDir = [
- path: { "${params.outdir}/compartments/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- ext.args = '--bigwig'
- }
+ //********************************
+ // COMPARTMENTS
- //********************************
- // TADS
+ withName: 'CALL_COMPARTMENTS' {
+ publishDir = [
+ path: { "${params.outdir}/compartments/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ ext.args = '--bigwig'
+ }
- withName: 'INSULATION' {
- publishDir = [
- path: { "${params.outdir}/tads/insulation/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- ext.args = '15 25 50 --window-pixels'
- }
+ //********************************
+ // TADS
- withName: 'HIC_FIND_TADS' {
- publishDir = [
- path: { "${params.outdir}/tads/hicExplorer" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- ext.args = '--correctForMultipleTesting fdr'
- }
+ withName: 'INSULATION' {
+ publishDir = [
+ path: { "${params.outdir}/tads/insulation/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ ext.args = '15 25 50 --window-pixels'
+ }
+
+ withName: 'HIC_FIND_TADS' {
+ publishDir = [
+ path: { "${params.outdir}/tads/hicExplorer" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ ext.args = '--correctForMultipleTesting fdr'
+ }
}
diff --git a/conf/test.config b/conf/test.config
index 47fb1674bfeb91da46f1a630ddf59988edc56967..59059aa6a4c826bb9c384a4234d9a2574c92daff 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -11,35 +11,32 @@
*/
params {
- config_profile_name = 'Hi-C test data from Schalbetter et al. (2017)'
- config_profile_description = 'Minimal test dataset to check pipeline function'
+ config_profile_name = 'Hi-C test data from Schalbetter et al. (2017)'
+ config_profile_description = 'Minimal test dataset to check pipeline function'
- // Limit resources so that this can run on Travis
- max_cpus = 2
- max_memory = 4.GB
- max_time = 1.h
+ // Limit resources so that this can run on Travis
+ max_cpus = 2
+ max_memory = 4.GB
+ max_time = 1.h
- // Input data
- //input_paths = [
- // ['SRR4292758_00', ['https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz']]
- // ]
- input = "${baseDir}/assets/samplesheet.csv"
+ // Input data
+ input = "${baseDir}/assets/samplesheet.csv"
- // Annotations
- fasta = 'https://github.com/nf-core/test-datasets/raw/hic/reference/W303_SGD_2015_JRIU00000000.fsa'
- digestion = 'hindiii'
- min_mapq = 10
- min_restriction_fragment_size = 100
- max_restriction_fragment_size = 100000
- min_insert_size = 100
- max_insert_size = 600
+ // Annotations
+ fasta = 'https://github.com/nf-core/test-datasets/raw/hic/reference/W303_SGD_2015_JRIU00000000.fsa'
+ digestion = 'hindiii'
+ min_mapq = 10
+ min_restriction_fragment_size = 100
+ max_restriction_fragment_size = 100000
+ min_insert_size = 100
+ max_insert_size = 600
- bin_size = '2000,1000'
- res_dist_decay = '1000'
- res_tads = '1000'
- tads_caller = 'insulation,hicexplorer'
- res_compartments = '2000'
+ bin_size = '2000,1000'
+ res_dist_decay = '1000'
+ res_tads = '1000'
+ tads_caller = 'insulation,hicexplorer'
+ res_compartments = '2000'
- // Ignore `--input` as otherwise the parameter validation will throw an error
- schema_ignore_params = 'genomes,digest,input_paths,input'
+ // Ignore `--input` as otherwise the parameter validation will throw an error
+ schema_ignore_params = 'genomes,digest,input_paths,input'
}