diff --git a/conf/modules.config b/conf/modules.config
index ff144483df14fede36406729bbfb8541139a9f82..7f4fceaf6bc79b61b4d142dcc4765feb4d13e446 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -100,7 +100,22 @@ process {
withName: 'MERGE_VALID_INTERACTION' {
publishDir = [
- path: { "${params.outdir}/hicpro/valid_pairs" },
+ [
+ path: { "${params.outdir}/hicpro/stats/" },
+ mode: 'copy',
+ pattern: "*stat"
+ ],
+ [
+ path: { "${params.outdir}/hicpro/valid_pairs" },
+ mode: 'copy',
+ pattern: "*Pairs"
+ ]
+ ]
+ }
+
+ withName: 'MERGE_STATS' {
+ publishDir = [
+ path: { "${params.outdir}/hicpro/stats" },
mode: 'copy'
]
}
diff --git a/modules/local/balance.nf~ b/modules/local/balance.nf~
deleted file mode 100644
index 728a04e10a5816ed6b1f76768e9a16c54cfb4543..0000000000000000000000000000000000000000
--- a/modules/local/balance.nf~
+++ /dev/null
@@ -1,31 +0,0 @@
-process COOLER_BALANCE {
- tag "$meta.id"
- label 'process_high'
-
- conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
- container "${ 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' }"
-
- input:
- tuple val(meta), path(cool)
-
- output:
- tuple val(meta), path("*.cool"), emit: cool
- path "versions.yml" , emit: versions
-
- script:
- def args = task.ext.args ?: ''
- """
- cp ${cool} ${cool.baseName}_norm.cool
- cooler balance \\
- $args \\
- -p ${task.cpus} \\
- ${cool.baseName}_norm.cool
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
- END_VERSIONS
- """
-}
diff --git a/modules/local/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
similarity index 100%
rename from modules/local/dnase_mapping_stats.nf
rename to modules/local/hicpro/dnase_mapping_stats.nf
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
new file mode 100644
index 0000000000000000000000000000000000000000..2ef759d1c9aa8b97652aef20e404dc3b65d492ec
--- /dev/null
+++ b/modules/local/hicpro/merge_stats.nf
@@ -0,0 +1,20 @@
+process MERGE_STATS {
+ label 'process_low'
+
+ input:
+ tuple val(meta), path(fstat)
+
+ output:
+ path("stats/"), emit:mqc_mstats
+ path("*stat"), emit:all_mstats
+
+ script:
+ if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" }
+ if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
+ if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
+ """
+ merge_statfiles.py -f ${fstat} > ${meta.id}.${ext}
+ mkdir -p stats/${meta.id}
+ cp ${meta.id}.${ext} stats/${meta.id}/
+ """
+}
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index 08196756536ed8a398b17569a97acad85a0aaee2..efc29ba1f65f87edb211acb8252b1f563ae15280 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/modules/local/hicpro/merge_valid_interaction.nf
@@ -8,7 +8,7 @@ process MERGE_VALID_INTERACTION {
output:
tuple val(meta), path("*.allValidPairs"), emit: valid_pairs
path("stats/"), emit:mqc
- path("*mergestat"), emit:stats
+ tuple val(meta), path("*mergestat"), emit:stats
script:
prefix = meta.id
diff --git a/modules/local/makebins.nf~ b/modules/local/makebins.nf~
deleted file mode 100644
index 4d3f307d404ca52338e3e9b429d6a4261983e53a..0000000000000000000000000000000000000000
--- a/modules/local/makebins.nf~
+++ /dev/null
@@ -1,30 +0,0 @@
-process COOLER_MAKEBINS {
- tag "$meta.id"
- label 'process_low'
-
- 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' }"
-
- input:
- tuple path(chromsizes), val(cool_bin)
-
- output:
- path ("*.bed") , emit: bed
- path "versions.yml", emit: versions
-
- script:
- def args = task.ext.args ?: ''
- """
- cooler makebins \\
- $args \\
- ${chromsizes} \\
- ${cool_bin} > cooler_bins_${cool_bin}.bed
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
- END_VERSIONS
- """
-}
diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf
deleted file mode 100644
index 336baa3df0ad3226113682a61fb5f9a73517b067..0000000000000000000000000000000000000000
--- a/modules/local/merge_stats.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-process merge_stats {
- tag "$ext"
- label 'process_low'
- publishDir "${params.outdir}/hicpro/", mode: params.publish_dir_mode,
- saveAs: {filename -> if (filename.endsWith("stat")) "stats/$filename"}
-
- input:
- tuple val(prefix), path(fstat)
-
- output:
- path("stats/"), emit:mqc_mstats
- path("*stat"), emit:all_mstats
-
- script:
- sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
- if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" }
- if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
- if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
- """
- merge_statfiles.py -f ${fstat} > ${prefix}.${ext}
- mkdir -p stats/${sample}
- cp ${prefix}.${ext} stats/${sample}/
- """
-}
diff --git a/modules/local/cooler_balance.nf b/modules/local/trash/cooler_balance.nf
similarity index 100%
rename from modules/local/cooler_balance.nf
rename to modules/local/trash/cooler_balance.nf
diff --git a/modules/local/cooler_raw.nf b/modules/local/trash/cooler_raw.nf
similarity index 100%
rename from modules/local/cooler_raw.nf
rename to modules/local/trash/cooler_raw.nf
diff --git a/modules/local/cooler_zoomify.nf b/modules/local/trash/cooler_zoomify.nf
similarity index 100%
rename from modules/local/cooler_zoomify.nf
rename to modules/local/trash/cooler_zoomify.nf
diff --git a/modules/local/makeBowtie2Index.nf b/modules/local/trash/makeBowtie2Index.nf
similarity index 100%
rename from modules/local/makeBowtie2Index.nf
rename to modules/local/trash/makeBowtie2Index.nf
diff --git a/nextflow.config b/nextflow.config
index 586c6b4ff1a5cda58efb1f5539d409ccb49b3297..1a413b7365ae1222599a798317cd6adb4d049a01 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -68,7 +68,7 @@ params {
// Contact maps
save_raw_maps = false
bin_size = '1000000'
- res_zoomify = '5000'
+ res_zoomify = false
hicpro_maps = false
ice_max_iter = 100
ice_filter_low_count_perc = 0.02
diff --git a/subworkflows/local/cooler.nf b/subworkflows/local/cooler.nf
index e24aed4eddb1063285c0df44fba6f0000d5245d0..897b0575e827e731b2e703ea0c73d2f9a2bd470c 100644
--- a/subworkflows/local/cooler.nf
+++ b/subworkflows/local/cooler.nf
@@ -28,7 +28,8 @@ workflow COOLER {
COOLER_MAKEBINS(
chromsize.combine(cool_bins)
)
-
+ ch_versions = ch_versions.mix(COOLER_MAKEBINS.out.versions)
+
//*****************************************
// BUILD COOL FILE PER RESOLUTION
// [meta, pairs, resolution]
@@ -37,14 +38,21 @@ workflow COOLER {
pairs.combine(cool_bins),
chromsize.collect()
)
+ ch_versions = ch_versions.mix(COOLER_CLOAD.out.versions)
COOLER_BALANCE(
COOLER_CLOAD.out.cool
)
+ ch_versions = ch_versions.mix(COOLER_BALANCE.out.versions)
// Zoomify at minimum bin resolution
+ if (!params.res_zoomify){
+ ch_res_zoomify = cool_bins.min()
+ }else{
+ ch_res_zoomify = params.res_zoomify
+ }
COOLER_CLOAD.out.cool
- .combine(cool_bins.min())
+ .combine(ch_res_zoomify)
.filter{ it [1] == it[3] }
.map{it->[it[0], it[2]]}
.set{ch_cool_zoomify}
@@ -52,6 +60,7 @@ workflow COOLER {
COOLER_ZOOMIFY(
ch_cool_zoomify
)
+ ch_versions = ch_versions.mix(COOLER_ZOOMIFY.out.versions)
//*****************************************
// DUMP DATA
@@ -60,6 +69,7 @@ workflow COOLER {
COOLER_DUMP(
COOLER_BALANCE.out.cool.map{[it[0], "", it[2]]}
)
+ ch_versions = ch_versions.mix(COOLER_DUMP.out.versions)
//COOLER_DUMP(
// COOLER_ZOOMIFY.out.mcool.combine(cool_bins).map{it->[it[0], it[2], it[1]]}
@@ -68,6 +78,7 @@ workflow COOLER {
SPLIT_COOLER_DUMP(
COOLER_DUMP.out.bedpe
)
+ ch_versions = ch_versions.mix(SPLIT_COOLER_DUMP.out.versions)
emit:
versions = ch_versions
diff --git a/subworkflows/local/hicpro.nf b/subworkflows/local/hicpro.nf
index 7ea1bcceb646c83832706dd6e1c415ddcfe2d2e0..3869d4df9de7538ad3b2fad09296e1cf4e9d9538 100644
--- a/subworkflows/local/hicpro.nf
+++ b/subworkflows/local/hicpro.nf
@@ -7,6 +7,7 @@
include { HICPRO_MAPPING } from './hicpro_mapping'
include { GET_VALID_INTERACTION } from '../../modules/local/hicpro/get_valid_interaction'
include { MERGE_VALID_INTERACTION } from '../../modules/local/hicpro/merge_valid_interaction'
+include { MERGE_STATS } from '../../modules/local/hicpro/merge_stats'
include { HICPRO2PAIRS } from '../../modules/local/hicpro/hicpro2pairs'
include { BUILD_CONTACT_MAPS } from '../../modules/local/hicpro/build_contact_maps'
include { ICE_NORMALIZATION } from '../../modules/local/hicpro/run_ice'
@@ -30,26 +31,39 @@ workflow HICPRO {
index,
ligation_site
)
+ ch_versions = ch_versions.mix(HICPRO_MAPPING.out.versions)
// get valid interaction
GET_VALID_INTERACTION (
HICPRO_MAPPING.out.bam,
fragments
)
-
+ //TODO ch_versions = ch_versions.mix(GET_VALID_INTERACTION.out.versions)
+
// merge valid interactions and remove duplicates
MERGE_VALID_INTERACTION (
GET_VALID_INTERACTION.out.valid_pairs
)
+ // TODO ch_versions = ch_versions.mix(MERGE_VALID_INTERACTION.out.versions)
+
+ // merge stats
+ HICPRO_MAPPING.out.mapstats.groupTuple()
+ .concat(HICPRO_MAPPING.out.pairstats.groupTuple(),
+ GET_VALID_INTERACTION.out.stats.groupTuple())
+ .view()
+ .set{ ch_hicpro_stats }
+
+ MERGE_STATS(
+ ch_hicpro_stats
+ )
+ //TODO ch_versions = ch_versions.mix(MERGE_STATS.out.versions)
// convert to pairs
HICPRO2PAIRS (
MERGE_VALID_INTERACTION.out.valid_pairs,
chrsize
)
-
- //merge stats
- // TODO
+ //TODO ch_versions = ch_versions.mix(HICPRO2PAIRS.out.versions)
if (params.hicpro_maps){
@@ -58,11 +72,13 @@ workflow HICPRO {
MERGE_VALID_INTERACTION.out.valid_pairs.combine(map_res),
chrsize.collect()
)
-
+ //TODO ch_versions = ch_versions.mix(BUILD_CONTACT_MAPS.out.versions)
+
// run_ice
ICE_NORMALIZATION(
BUILD_CONTACT_MAPS.out.maps
)
+ //TODO ch_versions = ch_versions.mix(ICE_NORMALIZATION.out.versions)
}
emit:
diff --git a/subworkflows/local/hicpro_mapping.nf b/subworkflows/local/hicpro_mapping.nf
index daa53c67306c0e79d7c4ec72ff7dd59394daa97e..0add95df88cd7fdc4bf6ce5538969cf221fcb116 100644
--- a/subworkflows/local/hicpro_mapping.nf
+++ b/subworkflows/local/hicpro_mapping.nf
@@ -84,6 +84,7 @@ workflow HICPRO_MAPPING {
MERGE_BOWTIE2(
ch_bowtie2_align
)
+ //TODO ch_versions = ch_versions.mix(MERGE_BOWTIE2.out.versions)
// Combine mates
MERGE_BOWTIE2.out.bam
@@ -95,8 +96,11 @@ workflow HICPRO_MAPPING {
COMBINE_MATES (
ch_bams
)
-
+ //TODO ch_versions = ch_versions.mix(COMBINE_MATES.out.versions)
+
emit:
versions = ch_versions
bam = COMBINE_MATES.out.bam
+ mapstats = MERGE_BOWTIE2.out.stats
+ pairstats = COMBINE_MATES.out.stats
}