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Commit fe439e9d authored by nservant's avatar nservant
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fix bug in igenomes

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conf/hicpro.config
+ 3
− 5
View file @ fe439e9d
......@@ -9,10 +9,6 @@
params {
// Reference
chromosome_size = false
bwt2_index = false
// Alignment options
bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'
bwt2_opts_trimmed = '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'
......@@ -20,7 +16,6 @@ params {
// Digestion Hi-C
restriction_site = 'A^AGGCT'
restriction_fragments = false
ligation_site = 'AAGCTAGCTT'
min_restriction_fragment_size = 0
max_restriction_fragment_size = 100
......@@ -39,5 +34,8 @@ params {
ice_filer_low_count_perc = 0.02
ice_filer_high_count_perc = 0
ice_eps = 0.1
saveReference = false
saveAlignedIntermediates = false
}
conf/igenomes.config
+ 22
− 22
View file @ fe439e9d
......@@ -12,91 +12,91 @@ params {
genomes {
'GRCh37' {
fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome"
}
'GRCm38' {
fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/genome"
}
'TAIR10' {
fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/genome"
}
'EB2' {
fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/genome"
}
'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/genome"
bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/genome"
}
'WBcel235' {
fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/genome"
}
'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/genome"
bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/genome"
}
'GRCz10' {
fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/genome"
}
'BDGP6' {
fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/genome"
}
'EquCab2' {
fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/genome"
}
'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/genome"
bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/genome"
}
'Galgal4' {
fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/genome"
}
'Gm01' {
fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/genome"
}
'Mmul_1' {
fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/genome"
}
'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/genome"
bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/genome"
}
'CHIMP2.1.4' {
fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/genome"
}
'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/genome"
bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/genome"
}
'R64-1-1' {
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome"
}
'EF2' {
fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/genome"
}
'Sbi1' {
fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/genome"
}
'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/genome"
bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/genome"
}
'AGPv3' {
fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/genome"
bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/genome"
}
}
}
conf/test.config
+ 2
− 2
View file @ fe439e9d
......@@ -19,8 +19,8 @@ params {
// Input data
readPaths = [
['SRR400264_00', ['https://github.com/nf-core/test-datasets/raw/hic/testdata/SRR400264_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/testdata/SRR400264_00_R2.fastq.gz']],
['SRR400264_01', ['https://github.com/nf-core/test-datasets/raw/hic/testdata/SRR400264_01_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/testdata/SRR400264_01_R2.fastq.gz']]
['SRR400264_00', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R2.fastq.gz']],
['SRR400264_01', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R2.fastq.gz']]
]
// Annotations
......
main.nf
+ 38
− 27
View file @ fe439e9d
......@@ -102,9 +102,10 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome
// Reference index path configuration
// Define these here - after the profiles are loaded with the iGenomes paths
params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
//params.chromosome_size = false
//params.restriction_fragments = false
// Has the run name been specified by the user?
// this has the bonus effect of catching both -name and --name
......@@ -175,13 +176,20 @@ if (params.readPaths){
// Reference genome
if ( params.bwt2_index ){
bwt2_file = file("${params.bwt2_index}.1.bt2")
if( !bwt2_file.exists() ) exit 1, "Reference genome Bowtie 2 not found: ${params.bwt2_index}"
bwt2_index = Channel.value( "${params.bwt2_index}" )
lastPath = params.bwt2_index.lastIndexOf(File.separator)
bwt2_dir = params.bwt2_index.substring(0,lastPath+1)
bwt2_base = params.bwt2_index.substring(lastPath+1)
Channel.fromPath( bwt2_dir, checkIfExists: true )
.ifEmpty { exit 1, "Genome index: Provided index not found: ${params.bwt2_index}" }
.into { bwt2_index_end2end; bwt2_index_trim }
}
else if ( params.fasta ) {
Channel.fromPath(params.fasta)
.ifEmpty { exit 1, "Fasta file not found: ${params.fasta}" }
lastPath = params.fasta.lastIndexOf(File.separator)
bwt2_base = params.fasta.substring(lastPath+1)
Channel.fromPath( params.fasta, checkIfExists: true )
.ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
.set { fasta_for_index }
}
else {
......@@ -191,11 +199,12 @@ else {
// Chromosome size
if ( params.chromosome_size ){
chromosome_size = Channel.value( "${params.chromosome_size}" )
Channel.FromPath( params.chromosome_size, checkIfExists: true )
.set {chromosome_size}
}
else if ( params.fasta ){
Channel.fromPath(params.fasta)
.ifEmpty { exit 1, "Fasta file not found: ${params.fasta}" }
Channel.fromPath( params.fasta, checkIfExists: true )
.ifEmpty { exit 1, "Chromosome sizes: Fasta file not found: ${params.fasta}" }
.set { fasta_for_chromsize }
}
else {
......@@ -204,11 +213,12 @@ else {
// Restriction fragments
if ( params.restriction_fragments ){
res_frag_file = Channel.value( "${params.restriction_fragments}" )
Channel.FromPath( params.restriction_fragments, checkIfExists: true )
.set {res_frag_file}
}
else if ( params.fasta && params.restriction_site ){
Channel.fromPath(params.fasta)
.ifEmpty { exit 1, "Fasta file not found: ${params.fasta}" }
Channel.fromPath(params.fasta, checkIfExists: true)
.ifEmpty { exit 1, "Restriction fragments: Fasta file not found: ${params.fasta}" }
.set { fasta_for_resfrag }
}
else {
......@@ -309,8 +319,8 @@ process get_software_versions {
if(!params.bwt2_index && params.fasta){
process makeBowtieIndex {
tag "$fasta"
publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.saveReference ? it : null }, mode: 'copy'
//publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
// saveAs: { params.saveReference ? it : null }, mode: 'copy'
input:
file fasta from fasta_for_index
......@@ -321,6 +331,7 @@ if(!params.bwt2_index && params.fasta){
script:
"""
mkdir bwt2_index
"""
}
}
......@@ -329,8 +340,8 @@ if(!params.bwt2_index && params.fasta){
if(!params.chromosome_size && params.fasta){
process makeChromSize {
tag "$fasta"
publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.saveReference ? it : null }, mode: 'copy'
//publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
// saveAs: { params.saveReference ? it : null }, mode: 'copy'
input:
file fasta from fasta_for_chromsize
......@@ -348,18 +359,18 @@ if(!params.chromosome_size && params.fasta){
if(!params.restriction_fragments && params.fasta){
process makeRestrictionFragments {
tag "$fasta"
publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.saveReference ? it : null }, mode: 'copy'
//publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
// saveAs: { params.saveReference ? it : null }, mode: 'copy'
input:
file fasta from fasta_for_resfrag
output:
file "*.bed" into restriction_fragments
file "*.bed" into res_frag_file
script:
"""
python digest_genome.py -r ${params.restriction_site} -o restriction_fragments.bed ${fasta}
digest_genome.py -r ${params.restriction_site} -o restriction_fragments.bed ${fasta}
"""
}
}
......@@ -378,7 +389,7 @@ process bowtie2_end_to_end {
tag "$prefix"
input:
set val(sample), file(reads) from raw_reads
val bt2_index from bwt2_index
file index from bwt2_index_end2end
output:
set val(prefix), file("${prefix}_unmap.fastq") into unmapped_end_to_end
......@@ -391,7 +402,7 @@ process bowtie2_end_to_end {
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${bwt2_opts} \\
-p ${task.cpus} \\
-x ${bt2_index} \\
-x ${index}/${bwt2_base} \\
--un ${prefix}_unmap.fastq \\
-U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
"""
......@@ -417,7 +428,7 @@ process bowtie2_on_trimmed_reads {
tag "$prefix"
input:
set val(prefix), file(reads) from trimmed_reads
val bt2_index from bwt2_index
file index from bwt2_index_trim
output:
set val(prefix), file("${prefix}_trimmed.bam") into trimmed_bam
......@@ -428,7 +439,7 @@ process bowtie2_on_trimmed_reads {
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${params.bwt2_opts_trimmed} \\
-p ${task.cpus} \\
-x ${bt2_index} \\
-x ${index}/${bwt2_base} \\
-U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
"""
}
......@@ -516,7 +527,7 @@ process build_contact_maps{
tag "$sample - $mres"
input:
set val(sample), file(vpairs), val(mres) from valid_pairs.combine(map_res)
val chrsize from chr_size
val chrsize from chromosome_size
output:
file("*.matrix") into raw_maps
......@@ -557,7 +568,7 @@ process generate_cool{
tag "$sample"
input:
set val(sample), file(vpairs) from valid_pairs_4cool
val chrsize from chr_size
val chrsize from chromosome_size
output:
file("*mcool") into cool_maps
......
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