From f17ea6ff25bd2229464e64c6594ad34098d2b2ea Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 28 Feb 2022 19:26:23 +0100
Subject: [PATCH] [MODIF] update cooltools
---
conf/modules.config | 21 +++++++++-
modules/local/compartment_calling.nf | 30 --------------
modules/local/{ => cooler}/balance.nf | 0
modules/local/{ => cooler}/makebins.nf | 0
modules/local/cooltools/eigs-cis.nf | 30 ++++++++++++++
modules/local/cooltools/insulation.nf | 26 ++++++++++++
modules/local/tads_insulation.nf | 25 -----------
modules/local/{ => trash}/functions.nf | 0
subworkflows/local/compartments.nf | 24 +++++++----
subworkflows/local/cooler.nf | 4 +-
subworkflows/local/tads.nf | 29 +++++++++----
workflows/hic.nf | 57 +++++++++++++++++++++++---
12 files changed, 166 insertions(+), 80 deletions(-)
delete mode 100644 modules/local/compartment_calling.nf
rename modules/local/{ => cooler}/balance.nf (100%)
rename modules/local/{ => cooler}/makebins.nf (100%)
create mode 100644 modules/local/cooltools/eigs-cis.nf
create mode 100644 modules/local/cooltools/insulation.nf
delete mode 100644 modules/local/tads_insulation.nf
rename modules/local/{ => trash}/functions.nf (100%)
diff --git a/conf/modules.config b/conf/modules.config
index 7f4fcea..9cef5f9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -204,4 +204,23 @@ process {
]
ext.args = "--balance"
}
-}
+
+ //********************************
+ // COMPARTMENTS
+
+ withName: 'CALL_COMPARTMENTS' {
+ ext.args = '--bigwig'
+ }
+
+ //********************************
+ // TADS
+
+ withName: 'INSULATION' {
+ ext.args = '15 25 50 --window-pixels'
+ }
+
+ withName: 'HIC_FIND_TADS' {
+ ext.args = '--correctForMultipleTesting fdr'
+ }
+
+}
\ No newline at end of file
diff --git a/modules/local/compartment_calling.nf b/modules/local/compartment_calling.nf
deleted file mode 100644
index 51f9788..0000000
--- a/modules/local/compartment_calling.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-process compartment_calling {
- tag "$sample - $res"
- label 'process_medium'
- publishDir "${params.outdir}/compartments", mode: 'copy'
-
- when:
- !params.skip_compartments
-
- input:
- tuple val(sample), val(res), path(cool), val(r)
- path(fasta)
- path(chrsize)
-
- output:
- path("*compartments*") optional true, emit:out_compartments
-
- script:
- """
- cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
- cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
- cooltools call-compartments --contact-type cis -o ${sample}_compartments ${cool}
- awk -F"\t" 'NR>1{OFS="\t"; if(\$6==""){\$6=0}; print \$1,\$2,\$3,\$6}' ${sample}_compartments.cis.vecs.tsv | sort -k1,1 -k2,2n > ${sample}_compartments.cis.E1.bedgraph
- """
-}
diff --git a/modules/local/balance.nf b/modules/local/cooler/balance.nf
similarity index 100%
rename from modules/local/balance.nf
rename to modules/local/cooler/balance.nf
diff --git a/modules/local/makebins.nf b/modules/local/cooler/makebins.nf
similarity index 100%
rename from modules/local/makebins.nf
rename to modules/local/cooler/makebins.nf
diff --git a/modules/local/cooltools/eigs-cis.nf b/modules/local/cooltools/eigs-cis.nf
new file mode 100644
index 0000000..74cd265
--- /dev/null
+++ b/modules/local/cooltools/eigs-cis.nf
@@ -0,0 +1,30 @@
+/*
+ * cooltools - call_compartments
+ */
+
+process CALL_COMPARTMENTS {
+ label 'process_medium'
+
+ input:
+ tuple val(meta), val(res), path(cool)
+ path(fasta)
+ path(chrsize)
+
+ output:
+ path("*compartments*"), emit: results
+ path("versions.yml"), emit: versions
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
+ cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
+ cooltools eigs-cis ${args} -o ${prefix}_compartments ${cool}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ cooltools: \$(cooltools --version 2>&1 | sed 's/cooletools, version //')
+ END_VERSIONS
+ """
+}
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
new file mode 100644
index 0000000..531bab9
--- /dev/null
+++ b/modules/local/cooltools/insulation.nf
@@ -0,0 +1,26 @@
+/*
+ * Cooltools - diamond-insulation
+ */
+
+process INSULATION {
+ label 'process_medium'
+
+ input:
+ tuple val(meta), path(cool)
+
+ output:
+ path("*tsv"), emit:results
+ path("versions.yml"), emit:versions
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ cooltools insulation ${cool} ${args} > ${prefix}_insulation.tsv
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ cooltools: \$(cooltools --version 2>&1 | sed 's/cooltools, version //')
+ END_VERSIONS
+ """
+}
diff --git a/modules/local/tads_insulation.nf b/modules/local/tads_insulation.nf
deleted file mode 100644
index 7338cd3..0000000
--- a/modules/local/tads_insulation.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-process tads_insulation {
- tag "$sample - $res"
- label 'process_medium'
- publishDir "${params.outdir}/tads/insulation", mode: 'copy'
-
- when:
- !params.skip_tads && params.tads_caller =~ 'insulation'
-
- input:
- tuple val(sample), val(res), path(cool), val(r)
-
- output:
- path("*tsv"), emit:insulation_tads
-
- script:
- """
- cooltools diamond-insulation --window-pixels ${cool} 15 25 50 > ${sample}_insulation.tsv
- """
-}
diff --git a/modules/local/functions.nf b/modules/local/trash/functions.nf
similarity index 100%
rename from modules/local/functions.nf
rename to modules/local/trash/functions.nf
diff --git a/subworkflows/local/compartments.nf b/subworkflows/local/compartments.nf
index e3089f3..23d78ac 100644
--- a/subworkflows/local/compartments.nf
+++ b/subworkflows/local/compartments.nf
@@ -1,15 +1,23 @@
-params.options = [:]
-
-include { COMPARTMENT_CALLING } from '../../modules/local/compartment_calling' addParams( options: params.options )
+include { CALL_COMPARTMENTS } from '../../modules/local/cooltools/eigs-cis'
workflow COMPARTMENTS {
- take:
+ take:
+ cool
+ fasta
+ chrsize
+ main:
+ ch_versions = Channel.empty()
- main:
-
+ CALL_COMPARTMENTS (
+ cool,
+ fasta.collect(),
+ chrsize.collect()
+ )
+ ch_versions = ch_versions.mix(CALL_COMPARTMENTS.out.versions)
- emit:
-
+ emit:
+ versions = ch_versions
+ compartments = CALL_COMPARTMENTS.out.results
}
\ No newline at end of file
diff --git a/subworkflows/local/cooler.nf b/subworkflows/local/cooler.nf
index 897b057..5c61d87 100644
--- a/subworkflows/local/cooler.nf
+++ b/subworkflows/local/cooler.nf
@@ -8,9 +8,9 @@ include { COOLER_CLOAD } from '../../modules/nf-core/modules/cooler/cload/main'
include { COOLER_DUMP } from '../../modules/nf-core/modules/cooler/dump/main'
include { COOLER_ZOOMIFY } from '../../modules/nf-core/modules/cooler/zoomify/main'
-include { COOLER_BALANCE } from '../../modules/local/balance'
+include { COOLER_BALANCE } from '../../modules/local/cooler/balance'
include { SPLIT_COOLER_DUMP } from '../../modules/local/split_cooler_dump'
-include { COOLER_MAKEBINS } from '../../modules/local/makebins'
+include { COOLER_MAKEBINS } from '../../modules/local/cooler/makebins'
workflow COOLER {
diff --git a/subworkflows/local/tads.nf b/subworkflows/local/tads.nf
index 9f0836a..496e8d6 100644
--- a/subworkflows/local/tads.nf
+++ b/subworkflows/local/tads.nf
@@ -1,16 +1,27 @@
-params.options = [:]
-
-include { TADS_HICEXPLORER } from '../../modules/local/tads_hicexplorer' addParams( options: params.options )
-include { TADS_INSULATION } from '../../modules/local/tads_insulation' addParams( options: params.options )
+include { INSULATION } from '../../modules/local/cooltools/insulation'
+include { HIC_FIND_TADS } from '../../modules/local/hicexplorer/hicFindTADs'
workflow TADS {
- take:
+ take:
+ cool
+ main:
+ ch_versions = Channel.empty()
+ ch_tads = Channel.empty()
- main:
-
+ if (params.tads_caller =~ 'insulation'){
+ INSULATION(cool)
+ ch_versions = ch_versions.mix(INSULATION.out.versions)
+ ch_tads = ch_tads.mix(INSULATION.out.results)
+ }
+
+ if (params.tads_caller =~ 'hicexplorer'){
+ HIC_FIND_TADS(cool)
+ ch_versions = ch_versions.mix(HIC_FIND_TADS.out.versions)
+ ch_tads = ch_tads.mix(HIC_FIND_TADS.out.results)
+ }
- emit:
-
+ emit:
+ tads = ch_tads
}
\ No newline at end of file
diff --git a/workflows/hic.nf b/workflows/hic.nf
index a65a385..0204db7 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -96,9 +96,9 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
//
// MODULE: Local to the pipeline
//
-//include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions' addParams( options: [publish_files : ['tsv':'']] )
-//include { OUTPUT_DOCUMENTATION } from '../modules/local/output_documentation' addParams( options: [publish_files : ['tsv':'']] )
-
+//include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions'
+//include { OUTPUT_DOCUMENTATION } from '../modules/local/output_documentation'
+include { HIC_PLOT_DIST_VS_COUNTS } from '../modules/local/hicexplorer/hicPlotDistVsCounts'
//
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
//
@@ -106,8 +106,8 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
include { HICPRO } from '../subworkflows/local/hicpro'
include { COOLER } from '../subworkflows/local/cooler'
-//include { COMPARTMENTS } from '../subworkflows/local/compartments'
-//include { TADS } from '../subworkflows/local/tads'
+include { COMPARTMENTS } from '../subworkflows/local/compartments'
+include { TADS } from '../subworkflows/local/tads'
/*
========================================================================================
@@ -190,6 +190,53 @@ workflow HIC {
ch_map_res
)
+ //
+ // MODULE: HICEXPLORER/HIC_PLOT_DIST_VS_COUNTS
+ //
+ if (!params.skip_dist_decay){
+ COOLER.out.cool
+ .combine(ch_ddecay_res)
+ .filter{ it[1] == it[3] }
+ .map { it -> [it[0], it[2]]}
+ .set{ ch_distdecay }
+
+ HIC_PLOT_DIST_VS_COUNTS(
+ ch_distdecay
+ )
+ }
+
+ //
+ // SUB-WORKFLOW: COMPARTMENT CALLING
+ //
+ if (!params.skip_compartments){
+ COOLER.out.cool
+ .combine(ch_comp_res)
+ .filter{ it[1] == it[3] }
+ .map { it -> [it[0], it[1], it[2]]}
+ .set{ ch_cool_compartments }
+
+ COMPARTMENTS(
+ ch_cool_compartments,
+ ch_fasta,
+ PREPARE_GENOME.out.chromosome_size
+ )
+ }
+
+ //
+ // SUB-WORKFLOW : TADS CALLING
+ //
+ if (!params.skip_tads){
+ COOLER.out.cool
+ .combine(ch_tads_res)
+ .filter{ it[1] == it[3] }
+ .map { it -> [it[0], it[2]]}
+ .set{ ch_cool_tads }
+
+ TADS(
+ ch_cool_tads
+ )
+ }
+
//
// MODULE: MultiQC
//
--
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