diff --git a/conf/test.config b/conf/test.config
index 5988a32428569c24f4f4d321ee727f617d3da202..08dfcfcba54efb1fa27a1d96b4ccde58afb94080 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -30,6 +30,8 @@ params {
min_insert_size = 100
max_insert_size = 600
- //hicexplorer does not run
+ bin_size = '10000'
+ //skip_mcool = true
+ //skip_tads = true
skip_dist_decay = true
}
diff --git a/main.nf b/main.nf
index 31691064a86ba38583cf0bab3b6cdbc6f1c1db7c..3f7c09d104e5c79ab73310090fe04f7a2e7589cf 100644
--- a/main.nf
+++ b/main.nf
@@ -243,25 +243,32 @@ else if (! params.dnase) {
exit 1, "No restriction fragments file specified!"
}
-
-if (params.res_tads){
+// Resolutions for contact maps
+map_res = Channel.from( params.bin_size ).splitCsv().flatten()
+all_res = params.bin_size
+if (params.res_tads && !params.skip_tads){
Channel.from( "${params.res_tads}" )
.splitCsv()
.flatten()
- .into {tads_res_hicexplorer; tads_res_insulation; tads_bin }
+ .into {tads_bin; tads_res_hicexplorer; tads_res_insulation}
+ map_res = map_res.concat(tads_bin)
+ all_res = all_res + ',' + params.res_tads
}else{
- tads_res=Channel.create()
- tads_bin=Channel.create()
+ tads_res_hicexplorer=Channel.empty()
+ tads_res_insulation=Channel.empty()
+ tads_bin=Channel.empty()
if (!params.skip_tads){
log.warn "[nf-core/hic] Hi-C resolution for TADs calling not specified. See --res_tads"
}
}
-if (params.res_dist_decay){
+if (params.res_dist_decay && !params.skip_dist_decay){
Channel.from( "${params.res_dist_decay}" )
.splitCsv()
.flatten()
.into {ddecay_res; ddecay_bin }
+ map_res = map_res.concat(ddecay_bin)
+ all_res = all_res + ',' + params.res_dist_decay
}else{
ddecay_res = Channel.create()
ddecay_bin = Channel.create()
@@ -270,13 +277,9 @@ if (params.res_dist_decay){
}
}
-
-// Resolutions for contact maps
-map_res = Channel.from( params.bin_size ).splitCsv().flatten()
-map_res.concat(tads_bin, ddecay_bin)
+map_res
.unique()
- .into { map_res; map_res_cool }
-
+ .into { map_res_summary; map_res; map_res_cool }
/**********************************************************
* SET UP LOGS
@@ -307,7 +310,7 @@ if (params.restriction_site){
summary['Min MAPQ'] = params.min_mapq
summary['Keep Duplicates'] = params.keep_dups ? 'Yes' : 'No'
summary['Keep Multihits'] = params.keep_multi ? 'Yes' : 'No'
-summary['Maps resolution'] = params.bin_size
+summary['Maps resolution'] = all_res
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir'] = params.outdir
@@ -458,7 +461,7 @@ if(!params.restriction_fragments && params.fasta && !params.dnase){
process bowtie2_end_to_end {
tag "$sample"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
input:
@@ -496,7 +499,7 @@ process bowtie2_end_to_end {
process trim_reads {
tag "$sample"
label 'process_low'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
when:
@@ -520,7 +523,7 @@ process trim_reads {
process bowtie2_on_trimmed_reads {
tag "$sample"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
when:
@@ -548,7 +551,7 @@ if (!params.dnase){
process bowtie2_merge_mapping_steps{
tag "$prefix = $bam1 + $bam2"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
input:
@@ -591,7 +594,7 @@ if (!params.dnase){
process dnase_mapping_stats{
tag "$sample = $bam"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
input:
@@ -623,7 +626,7 @@ if (!params.dnase){
process combine_mates{
tag "$sample = $r1_prefix + $r2_prefix"
label 'process_low'
- publishDir "${params.outdir}/mapping", mode: params.publish_dir_mode,
+ publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"}
input:
@@ -659,7 +662,7 @@ if (!params.dnase){
process get_valid_interaction{
tag "$sample"
label 'process_low'
- publishDir "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
+ publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
input:
@@ -698,7 +701,7 @@ else{
process get_valid_interaction_dnase{
tag "$sample"
label 'process_low'
- publishDir "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
+ publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
input:
@@ -730,7 +733,7 @@ else{
process remove_duplicates {
tag "$sample"
label 'process_highmem'
- publishDir "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
+ publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$sample/$filename" : "$filename"}
input:
@@ -776,7 +779,7 @@ process remove_duplicates {
process merge_stats {
tag "$ext"
label 'process_low'
- publishDir "${params.outdir}/stats/${sample}", mode: params.publish_dir_mode
+ publishDir "${params.outdir}/hicpro/stats/${sample}", mode: params.publish_dir_mode
input:
set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
@@ -982,7 +985,11 @@ process convert_to_h5 {
* Counts vs distance QC
*/
-chddecay = h5maps_ddecay.combine(ddecay_res).filter{ it[1] == it[3] }.dump(tag: "ddecay")
+if (!params.skip_dist_decay){
+ chddecay = h5maps_ddecay.combine(ddecay_res).filter{ it[1] == it[3] }.dump(tag: "ddecay")
+}else{
+ chddecay = Channel.empty()
+}
process dist_decay {
tag "$sample"
@@ -1013,7 +1020,11 @@ process dist_decay {
*/
/*
-chcomp = iced_maps_comp.combine(comp_res).filter{ it[1] == it[4] }.dump(tag: "comp")
+if(!params.skip_compartments){
+ chcomp = iced_maps_comp.combine(comp_res).filter{ it[1] == it[4] }.dump(tag: "comp")
+}else{
+ chcomp = Channel.empty()
+}
process compartment_calling {
tag "$sample - $res"
@@ -1041,7 +1052,11 @@ process compartment_calling {
* TADs calling
*/
-chtads = h5maps_tads.combine(tads_res_hicexplorer).filter{ it[1] == it[3] }.dump(tag: "hicexp")
+if (!params.skip_tads){
+ chtads = h5maps_tads.combine(tads_res_hicexplorer).filter{ it[1] == it[3] }.dump(tag: "hicexp")
+}else{
+ chtads = Channel.empty()
+}
process tads_hicexplorer {
tag "$sample - $res"
@@ -1066,7 +1081,11 @@ process tads_hicexplorer {
"""
}
-chIS = norm_cool_maps.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins")
+if (!params.skip_tads){
+ chIS = norm_cool_maps.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins")
+}else{
+ chIS = Channel.empty()
+}
process tads_insulation {
tag "$sample - $res"
diff --git a/nextflow.config b/nextflow.config
index 8cca55407e0507080912a66b28d2ff63541858b2..c3ddb3859d3957cab975eaa4f28fb1103e9fe06b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -59,14 +59,14 @@ params {
min_cis_dist = 0
// Contact maps
- bin_size = '1000000,500000'
+ bin_size = '1000000'
ice_max_iter = 100
ice_filer_low_count_perc = 0.02
ice_filer_high_count_perc = 0
ice_eps = 0.1
// Downstream Analysis
- res_dist_decay = '1000000'
+ res_dist_decay = '250000'
tads_caller = 'insulation'
res_tads = '40000'
res_zoomify = '5000'