diff --git a/bin/hicpro_merge_validpairs.sh b/bin/hicpro_merge_validpairs.sh
index 5f383c534753bf77b05665501453cb9d501bf2c0..09f97277aee9ee4e23199c2b996077db63e30464 100755
--- a/bin/hicpro_merge_validpairs.sh
+++ b/bin/hicpro_merge_validpairs.sh
@@ -10,8 +10,8 @@ rmDup=0
prefix=""
while getopts ":dp:" opt; do
case "$opt" in
- d) rmDup=1 ;;
- p) prefix=$OPTARG ;;
+ d) rmDup=1 ;;
+ p) prefix=$OPTARG ;;
esac
done
shift $(( OPTIND - 1 ))
@@ -21,11 +21,11 @@ vpairs="$@"
if [[ ${rmDup} == 1 ]]; then
## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
- awk -F"\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=$2 || c2!=$5 || s1!=$3 || s2!=$6){print;c1=$2;c2=$5;s1=$3;s2=$6}' > ${prefix}.allValidPairs
+ awk -F"\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=$2 || c2!=$5 || s1!=$3 || s2!=$6){print;c1=$2;c2=$5;s1=$3;s2=$6}' > ${prefix}.allValidPairs
else
cat ${vpairs} > ${prefix}.allValidPairs
fi
-
+
echo -e -n "valid_interaction\t" > ${prefix}_allValidPairs.mergestat
cat ${vpairs} | wc -l >> ${prefix}_allValidPairs.mergestat
echo -e -n "valid_interaction_rmdup\t" >> ${prefix}_allValidPairs.mergestat
diff --git a/bin/src/cutsite_trimming.cpp b/bin/src/cutsite_trimming.cpp
index 03cb20f3f74ff0282ad6560f029d0a9975fe517b..5cccebf4cd15500d41b746467681c8a218e29ac1 100644
--- a/bin/src/cutsite_trimming.cpp
+++ b/bin/src/cutsite_trimming.cpp
@@ -1,5 +1,5 @@
// HiC-Pro
-// Copyright 2015 Institut Curie
+// Copyright 2015 Institut Curie
// Author(s): Nicolas Servant
// Contact: nicolas.servant@curie.fr
// This software is distributed without any guarantee under the terms of the BSD-3 licence
@@ -21,8 +21,7 @@ static int usage(int ret=1)
return ret;
}
-static int get_options(int argc, char* argv[], std::string& fastqFile,
- std::vector<std::string>& cutSites, std::string& output, bool& rmuntrim)
+static int get_options(int argc, char* argv[], std::string& fastqFile, std::vector<std::string>& cutSites, std::string& output, bool& rmuntrim)
{
prog = argv[0];
if (argc == 1){
@@ -34,84 +33,82 @@ static int get_options(int argc, char* argv[], std::string& fastqFile,
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 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();
- }
+ std::cerr << prog << ": unknown option " << opt << std::endl;
+ return usage();
+ }
}
return 0;
}
-static int trim_fastq(std::string& fastqFile,
- std::vector<std::string>& cutSites,
- std::string& outFile, bool& rmuntrim){
+static int trim_fastq(std::string& fastqFile, std::vector<std::string>& cutSites, std::string& outFile, bool& rmuntrim){
int trim_count=0;
std::string ID;
std::ifstream ifs (fastqFile);
std::ofstream ofs (outFile);
-
+
if (ifs.is_open()){
while (getline(ifs, ID)) {
- std::string seq;
- std::string dummy;
- std::string qual;
-
- getline(ifs, seq);
- getline(ifs, dummy);
- getline(ifs, qual);
+ std::string seq;
+ std::string dummy;
+ std::string qual;
+
+ getline(ifs, seq);
+ getline(ifs, dummy);
+ getline(ifs, qual);
- bool find_pos = false;
- size_t pos = std::string::npos;
- for (std::vector<std::string>::iterator it = cutSites.begin(); it != cutSites.end(); ++it){
- size_t tmp_pos = seq.find(*it);
- if (tmp_pos != std::string::npos) {
- // If find_pos is alread True, there is a problem (there are two cut
- // sites in the same read).)
- if (find_pos == true){
- if(tmp_pos < pos) {
- pos = tmp_pos;
- }
- } else {
- find_pos = true;
- pos = tmp_pos;
- }
- }
- }
-
- if (pos != std::string::npos) {
- trim_count++;
- ofs << ID << '\n';
- ofs << seq.substr(0, pos) << '\n';
- ofs << "+\n";
- ofs << qual.substr(0, pos) << '\n';
- } else {
- if (!rmuntrim){
- ofs << ID << '\n';
- ofs << seq << '\n';
- ofs << "+\n";
- ofs << qual << '\n';
- }
- }
- find_pos = false;
- }
+ bool find_pos = false;
+ size_t pos = std::string::npos;
+ for (std::vector<std::string>::iterator it = cutSites.begin(); it != cutSites.end(); ++it){
+ size_t tmp_pos = seq.find(*it);
+ if (tmp_pos != std::string::npos) {
+ // If find_pos is alread True, there is a problem (there are two cut
+ // sites in the same read).)
+ if (find_pos == true){
+ if(tmp_pos < pos) {
+ pos = tmp_pos;
+ }
+ } else {
+ find_pos = true;
+ pos = tmp_pos;
+ }
+ }
+ }
+
+ if (pos != std::string::npos) {
+ trim_count++;
+ ofs << ID << '\n';
+ ofs << seq.substr(0, pos) << '\n';
+ ofs << "+\n";
+ ofs << qual.substr(0, pos) << '\n';
+ } else {
+ if (!rmuntrim){
+ ofs << ID << '\n';
+ ofs << seq << '\n';
+ ofs << "+\n";
+ ofs << qual << '\n';
+ }
+ }
+ find_pos = false;
+ }
}else{
std::cerr << "Error : Cannot open file : " << fastqFile;
}
@@ -135,7 +132,7 @@ int main(int argc, char* argv[])
if (fastqFile.empty() || cutSites.size() == 0 || outFile.empty()){
usage();
- exit(ret);
+ exit(ret);
}
int trim_count=trim_fastq(fastqFile, cutSites, outFile, rmuntrim);
@@ -144,4 +141,3 @@ int main(int argc, char* argv[])
}
-
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 61de40b1236b8be39ac009ff54f46d99ceebeab6..3b50325dd6c5c629fd80c79b540745b8127ad8a9 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -17,147 +17,147 @@ params {
}
'GRCh38' {
fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
- }
- 'GRCm38' {
+ bowtie2 = "${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' {
+ 'TAIR10' {
fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
- }
- 'EB2' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ 'GRCz10' {
fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
- }
- 'BDGP6' {
+ }
+ 'BDGP6' {
fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
- }
- 'EquCab2' {
+ }
+ 'EquCab2' {
fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
- }
- 'EB1' {
+ }
+ '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' {
+ }
+ 'Galgal4' {
fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
- }
- 'Gm01' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ 'EF2' {
fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
- }
- 'Sbi1' {
+ }
+ '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' {
+ }
+ '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' {
+ }
+ 'AGPv3' {
fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
- }
- 'hg38' {
+ }
+ 'hg38' {
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
- }
- 'hg19' {
+ }
+ 'hg19' {
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
- }
- 'mm10' {
+ }
+ 'mm10' {
fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
- }
- 'bosTau8' {
+ }
+ 'bosTau8' {
fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
- }
- 'ce10' {
+ }
+ 'ce10' {
fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
- }
- 'canFam3' {
+ }
+ 'canFam3' {
fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
- }
- 'danRer10' {
+ }
+ 'danRer10' {
fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
- }
- 'dm6' {
+ }
+ 'dm6' {
fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
- }
- 'equCab2' {
+ }
+ 'equCab2' {
fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
- }
- 'galGal4' {
+ }
+ 'galGal4' {
fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
- }
- 'panTro4' {
+ }
+ 'panTro4' {
fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
- }
- 'rn6' {
+ }
+ 'rn6' {
fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
- }
- 'sacCer3' {
+ }
+ 'sacCer3' {
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
- }
- 'susScr3' {
+ }
+ '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 32a65a438d07250e8db5020805b34197cbbb1cfc..13eb114c3baf28af2d51080349f299cd50f37025 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -48,8 +48,8 @@ process {
path: { "${params.outdir}/hicpro/mapping" },
mode: 'copy',
enabled: params.save_aligned_intermediates
- ]
- ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
+ ]
+ ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
ext.args = params.bwt2_opts_end2end ?: ''
ext.args2 = !params.dnase ? "-F 4" :""
}
@@ -68,9 +68,9 @@ process {
mode: 'copy',
enabled: params.save_aligned_intermediates
]
- ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}_trimmed" : "${meta.id}_${meta.mates}_trimmed" }
- ext.args = params.bwt2_opts_trimmed ?: ''
- ext.args2 = ""
+ ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}_trimmed" : "${meta.id}_${meta.mates}_trimmed" }
+ ext.args = params.bwt2_opts_trimmed ?: ''
+ ext.args2 = ""
}
withName: 'MERGE_BOWTIE2' {
@@ -79,20 +79,20 @@ process {
mode: 'copy',
enabled: params.save_aligned_intermediates
]
- ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
+ ext.prefix = { params.split_fastq ? "${meta.chunk}_${meta.mates}" : "${meta.id}_${meta.mates}" }
}
withName: 'COMBINE_MATES' {
publishDir = [
- path: { "${params.outdir}/hicpro/mapping" },
+ path: { "${params.outdir}/hicpro/mapping" },
mode: 'copy',
pattern: '*.bam'
- ]
+ ]
ext.args = [
"-t",
params.keep_multi ? "--multi" : "",
params.min_mapq ? "-q ${params.min_mapq}" : ""
- ].join(' ').trim()
+ ].join(' ').trim()
ext.prefix = { params.split_fastq ? "${meta.chunk}" : "${meta.id}" }
}
@@ -103,7 +103,7 @@ process {
mode: 'copy',
enabled: params.save_pairs_intermediates
]
- ext.args = { [
+ 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}" : '',
@@ -120,7 +120,7 @@ process {
mode: 'copy',
enabled: params.save_pairs_intermediates
]
- ext.args = { params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : "" }
+ ext.args = { params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : "" }
}
withName: 'MERGE_VALID_INTERACTION' {
@@ -134,10 +134,10 @@ process {
path: { "${params.outdir}/hicpro/valid_pairs" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- pattern: "*Pairs"
+ pattern: "*Pairs"
]
]
- ext.args = { params.keep_dups ? '' : '-d' }
+ ext.args = { params.keep_dups ? '' : '-d' }
}
withName: 'MERGE_STATS' {
@@ -167,7 +167,7 @@ process {
withName: 'ICE_NORMALIZATION' {
publishDir = [
- path: { "${params.outdir}/hicpro/matrix/iced" },
+ path: { "${params.outdir}/hicpro/matrix/iced" },
mode: 'copy',
enabled: params.hicpro_maps
]
@@ -189,9 +189,9 @@ process {
withName: 'COOLER_MAKEBINS' {
publishDir = [
- path: { "${params.outdir}/contact_maps/bins/" },
+ path: { "${params.outdir}/contact_maps/bins/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
+ mode: 'copy'
]
}
@@ -202,7 +202,7 @@ process {
mode: 'copy',
enabled : params.save_raw_maps
]
- ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
+ ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
}
withName: 'COOLER_BALANCE' {
@@ -211,15 +211,15 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
mode: 'copy'
]
- ext.args = '--force'
+ ext.args = '--force'
}
withName: 'COOLER_DUMP' {
publishDir = [
enabled: false
- ]
- ext.prefix = { "${cool.baseName}" }
- ext.args = "--one-based-ids --balanced --na-rep 0"
+ ]
+ ext.prefix = { "${cool.baseName}" }
+ ext.args = "--one-based-ids --balanced --na-rep 0"
}
withName:'SPLIT_COOLER_DUMP' {
@@ -228,14 +228,14 @@ process {
path: { "${params.outdir}/contact_maps/txt/" },
mode: 'copy',
pattern: "*_raw.txt",
- enabled: params.save_raw_maps
- ],
+ enabled: params.save_raw_maps
+ ],
[
path: { "${params.outdir}/contact_maps/txt/" },
- mode: 'copy',
- pattern: "*_balanced.txt"
+ mode: 'copy',
+ pattern: "*_balanced.txt"
]
- ]
+ ]
}
withName: 'COOLER_ZOOMIFY' {
@@ -255,8 +255,8 @@ process {
path: { "${params.outdir}/compartments/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
mode: 'copy'
- ]
- ext.args = '--bigwig'
+ ]
+ ext.args = '--bigwig'
}
//********************************
@@ -268,7 +268,7 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
mode: 'copy'
]
- ext.args = '15 25 50 --window-pixels'
+ ext.args = '15 25 50 --window-pixels'
}
withName: 'HIC_FIND_TADS' {
@@ -277,6 +277,6 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
mode: 'copy'
]
- ext.args = '--correctForMultipleTesting fdr'
+ ext.args = '--correctForMultipleTesting fdr'
}
}
diff --git a/conf/test.config b/conf/test.config
index 59059aa6a4c826bb9c384a4234d9a2574c92daff..1501b027bf9a0af965f021c6d85604de690834ff 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -36,7 +36,7 @@ params {
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'
}
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
index be8324b62b86f8dbdef3dcea81c4dda7206aa508..d2fae92e9b13224bd5352df9e769f05bba84386c 100755
--- a/lib/WorkflowHic.groovy
+++ b/lib/WorkflowHic.groovy
@@ -12,8 +12,8 @@ class WorkflowHic {
// digestion parameters
if (params.digest && params.digestion && !params.digest.containsKey(params.digestion)) {
- log.error "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
- System.exit(1)
+ log.error "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
+ System.exit(1)
}
// Check Digestion or DNase Hi-C mode
diff --git a/modules/local/cooler/balance.nf b/modules/local/cooler/balance.nf
index 37e808d0e5a1909775f9b6039a42eb069df7fe07..d03959a6ed764e79af2377ad0c501f1bc1b92b5b 100644
--- a/modules/local/cooler/balance.nf
+++ b/modules/local/cooler/balance.nf
@@ -23,7 +23,7 @@ process COOLER_BALANCE {
cooler balance \\
$args \\
-p ${task.cpus} \\
- ${cool}${suffix}
+ ${cool}${suffix}
cp ${cool} ${prefix}.${extension}
diff --git a/modules/local/cooler/makebins.nf b/modules/local/cooler/makebins.nf
index c956a6ae54b80916257a58e1d93c7a7adac98776..09147d45109b01fe256f59fcf7fdafcfaad33960 100644
--- a/modules/local/cooler/makebins.nf
+++ b/modules/local/cooler/makebins.nf
@@ -5,7 +5,7 @@ process COOLER_MAKEBINS {
conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+ 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple path(chromsizes), val(cool_bin)
@@ -19,8 +19,8 @@ process COOLER_MAKEBINS {
"""
cooler makebins \\
$args \\
- ${chromsizes} \\
- ${cool_bin} > cooler_bins_${cool_bin}.bed
+ ${chromsizes} \\
+ ${cool_bin} > cooler_bins_${cool_bin}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/local/cooltools/eigs-cis.nf b/modules/local/cooltools/eigs-cis.nf
index 6d77a87ecd1bfc0033a936b4ab92a265f17ed877..a63dee2eb39ca6a7e37f06a6d09c39a4971a47e5 100644
--- a/modules/local/cooltools/eigs-cis.nf
+++ b/modules/local/cooltools/eigs-cis.nf
@@ -1,7 +1,7 @@
/*
* cooltools - call_compartments
*/
-
+
process CALL_COMPARTMENTS {
label 'process_medium'
@@ -12,8 +12,8 @@ process CALL_COMPARTMENTS {
input:
tuple val(meta), path(cool), val(resolution)
- path(fasta)
- path(chrsize)
+ path(fasta)
+ path(chrsize)
output:
path("*compartments*"), emit: results
@@ -24,7 +24,7 @@ process CALL_COMPARTMENTS {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cooltools genome binnify --all-names ${chrsize} ${resolution} > genome_bins.txt
- cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
+ cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
cooltools eigs-cis ${args} -o ${prefix}_compartments ${cool}
cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index dc755acbc1b5bce48eb56afb65587f4772a67484..d6fd194810163729974567bb0c3bdfc2182dd607 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -1,14 +1,14 @@
/*
* Cooltools - diamond-insulation
*/
-
+
process INSULATION {
label 'process_medium'
conda (params.enable_conda ? "bioconda::cooltools=0.5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
- 'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
+ 'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
input:
tuple val(meta), path(cool)
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index 093484c24c99f5d3c07071681c5bd3b7808df992..a6705e28f700cf744b2ef7bebb1f522e035f58f9 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -1,14 +1,14 @@
/*
* hicexplorer - hicFindTADs
*/
-
+
process HIC_FIND_TADS {
label 'process_medium'
conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
- 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+ 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(cool)
@@ -22,9 +22,9 @@ process HIC_FIND_TADS {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
hicFindTADs --matrix ${cool} \
- --outPrefix ${prefix}_hicfindtads \
- ${args} \
- --numberOfProcessors ${task.cpus}
+ --outPrefix ${prefix}_hicfindtads \
+ ${args} \
+ --numberOfProcessors ${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index a426d12ea6583bcb91bf930454dc449824199ae1..4c7d05f40a4d5cfb486b6ea3748f668d2e88398a 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
@@ -1,7 +1,7 @@
/*
* hicexplorer - hicPlotDistVsCounts
*/
-
+
process HIC_PLOT_DIST_VS_COUNTS {
label 'process_medium'
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index 3ae9428c041228ec793f2511709df485cafb90df..752966dc91b7d95b4f67747a2052e32d3629baee 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/modules/local/hicpro/bowtie2_merge.nf
@@ -1,14 +1,14 @@
process MERGE_BOWTIE2{
tag "$prefix"
label 'process_medium'
-
+
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
-
+
input:
- tuple val(meta), path(bam1), path(bam2)
+ tuple val(meta), path(bam1), path(bam2)
output:
tuple val(meta), path("${prefix}_bwt2merged.bam"), emit: bam
@@ -20,13 +20,13 @@ process MERGE_BOWTIE2{
tag = meta.mates
"""
samtools merge -@ ${task.cpus} \\
- -f ${prefix}_bwt2merged.bam \\
- ${bam1} ${bam2}
+ -f ${prefix}_bwt2merged.bam \\
+ ${bam1} ${bam2}
samtools sort -@ ${task.cpus} -m 800M \\
- -n \\
- -o ${prefix}_bwt2merged.sorted.bam \\
- ${prefix}_bwt2merged.bam
+ -n \\
+ -o ${prefix}_bwt2merged.sorted.bam \\
+ ${prefix}_bwt2merged.bam
mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
@@ -44,5 +44,5 @@ process MERGE_BOWTIE2{
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
- """
+ """
}
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index e3587c1dde82bb07a52d28899698aea938d916d7..5d92f4b36ac5402ad3d5f4cfa66fac84b74ac4ce 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -4,9 +4,9 @@ process COMBINE_MATES {
conda (params.enable_conda ? "conda-forge::python=3.9 bioconda::pysam=0.19.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
-
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+
input:
tuple val(meta), path(bam)
@@ -23,7 +23,7 @@ process COMBINE_MATES {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+ python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
END_VERSIONS
"""
}
diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index bf0da6fb51e20c1f0d5be37425f22f97bb956883..edc40dc26329dee3334b66240a85e8803352032b 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/modules/local/hicpro/dnase_mapping_stats.nf
@@ -9,7 +9,7 @@ process MAPPING_STATS_DNASE {
input:
- tuple val(meta), path(bam)
+ tuple val(meta), path(bam)
output:
tuple val(meta), path(bam), emit:bam
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index ef56f9d342d35af4d015edf5b95a86ba313d54b5..055db6a3045dee93da371bdc2e2bbb0f8df65cae 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -4,11 +4,11 @@ process GET_RESTRICTION_FRAGMENTS {
conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::numpy=1.22.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
- path fasta
+ path fasta
val(res_site)
output:
@@ -21,7 +21,7 @@ process GET_RESTRICTION_FRAGMENTS {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+ python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
END_VERSIONS
"""
}
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index a2bfb84988072d2dd638a624c53d07e636103a49..2709cdee3530c26820708ef9fd341c424ea14b9a 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -4,11 +4,11 @@ process GET_VALID_INTERACTION {
conda (params.enable_conda ? "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
- tuple val(meta), path(bam)
+ tuple val(meta), path(bam)
path(resfrag)
output:
@@ -24,14 +24,14 @@ process GET_VALID_INTERACTION {
def args = task.ext.args ?: ''
"""
mapped_2hic_fragments.py \\
- -f ${resfrag} \\
- -r ${bam} \\
- --all \\
- ${args}
+ -f ${resfrag} \\
+ -r ${bam} \\
+ --all \\
+ ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+ python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
END_VERSIONS
"""
}
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index 983b85875c169be3351bd1ac3f984795713038ea..08a019f203653b25eaad601026c368e2e283d50c 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/modules/local/hicpro/get_valid_interaction_dnase.nf
@@ -4,11 +4,11 @@ process GET_VALID_INTERACTION_DNASE {
conda (params.enable_conda ? "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
-
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+
input:
- tuple val(meta), path(bam)
+ tuple val(meta), path(bam)
output:
tuple val(meta), path("*.validPairs"), emit:valid_pairs
@@ -19,12 +19,12 @@ process GET_VALID_INTERACTION_DNASE {
def args = task.ext.args ?: ''
"""
mapped_2hic_dnase.py \\
- -r ${bam} \\
- ${args}
+ -r ${bam} \\
+ ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+ python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
END_VERSIONS
"""
}
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index ddab40eefca7044436c2abc67898d4e9d354686b..4ee35b0c1715ec35adb731738e3fb6f26e9976ab 100644
--- a/modules/local/hicpro/hicpro2pairs.nf
+++ b/modules/local/hicpro/hicpro2pairs.nf
@@ -9,7 +9,7 @@ process HICPRO2PAIRS {
input:
tuple val(meta), path(vpairs)
- path chrsize
+ path chrsize
output:
tuple val(meta), path("*.pairs.gz"), path("*.pairs.gz.px2"), emit: pairs
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index c6cb940759e1bb48416614d2c6f3115865bd782a..743f3740f4a630a506c510cd4879c50844f51b7f 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -3,11 +3,11 @@ process MERGE_STATS {
conda (params.enable_conda ? "conda-forge::python=3.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
- tuple val(meta), path(fstat)
+ tuple val(meta), path(fstat)
output:
path("${meta.id}/"), emit: mqc
@@ -25,7 +25,7 @@ process MERGE_STATS {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+ python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
END_VERSIONS
"""
}
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index 371600c8ff4de2591adb92327d82ba9960e63a9b..6da435621a1835e667f8111935c74cd8f6e0c008 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/modules/local/hicpro/merge_valid_interaction.nf
@@ -4,11 +4,11 @@ process MERGE_VALID_INTERACTION {
conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+ 'ubuntu:20.04' }"
input:
- tuple val(meta), path(vpairs)
+ tuple val(meta), path(vpairs)
output:
tuple val(meta), path("*.allValidPairs"), emit: valid_pairs
@@ -28,7 +28,7 @@ process MERGE_VALID_INTERACTION {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- sort: \$(echo \$(sort --version 2>&1 | head -1 | awk '{print \$NF}' 2>&1))
+ sort: \$(echo \$(sort --version 2>&1 | head -1 | awk '{print \$NF}' 2>&1))
END_VERSIONS
"""
-}
+}
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index 466cd6b12e6daa9bf632a985586405c4991775e3..e77b5c240934dac3f034939fba2f58c1303e7af2 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -4,11 +4,11 @@ process ICE_NORMALIZATION{
conda (params.enable_conda ? "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
-
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+
input:
- tuple val(meta), val(res), path(rmaps), path(bed)
+ tuple val(meta), val(res), path(rmaps), path(bed)
output:
tuple val(meta), val(res), path("*iced.matrix"), path(bed), emit:maps
@@ -25,8 +25,8 @@ process ICE_NORMALIZATION{
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
- iced: \$(python -c "import iced; print(iced.__version__)")
+ python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+ iced: \$(python -c "import iced; print(iced.__version__)")
END_VERSIONS
"""
}
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index a4ba7d3307cd82a65e5c2e0dc2b4563e74bfef89..1585591f702ec578a91ffe05ade933a8fedf04da 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -6,9 +6,9 @@ process TRIM_READS {
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
-
+
input:
- tuple val(meta), path(reads)
+ tuple val(meta), path(reads)
val(motif)
output:
@@ -19,8 +19,8 @@ process TRIM_READS {
"""
zcat ${reads} > tmp.fastq
cutsite_trimming --fastq tmp.fastq \\
- --cutsite ${motif[0]} \\
- --out ${reads.simpleName}_trimmed.fastq
+ --cutsite ${motif[0]} \\
+ --out ${reads.simpleName}_trimmed.fastq
gzip ${reads.simpleName}_trimmed.fastq
/bin/rm -f tmp.fastq