diff --git a/conf/modules.config b/conf/modules.config
index 9eeb18147b19c714969e770b59102b98a87c11c6..6a5ccd5f19dfee8372954c388f64c103e10145a4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -212,6 +212,7 @@ process {
mode: 'copy'
]
ext.args = '--force'
+ ext.prefix = { "${meta.id}_balanced" }
}
withName: 'COOLER_DUMP' {
@@ -262,7 +263,7 @@ process {
//********************************
// TADS
- withName: 'COOLTOOS_INSULATION' {
+ withName: 'COOLTOOLS_INSULATION' {
publishDir = [
path: { "${params.outdir}/tads/insulation/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
diff --git a/modules.json b/modules.json
index 5d64e0f011b77c9222196542f0bf156f87d17cd9..7d1fc471f7b55fc00860edc5a89abe7d5027f23a 100644
--- a/modules.json
+++ b/modules.json
@@ -74,13 +74,6 @@
"installed_by": [
"modules"
]
- },
- "multiqc": {
- "branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
- "installed_by": [
- "modules"
- ]
}
}
},
diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf
index 9af2a4d09e1e47013eb10c2e4289f7f617b76eb4..29a099c4883d060f2fc551279f3edbd109ef5076 100644
--- a/modules/local/cooltools/eigscis.nf
+++ b/modules/local/cooltools/eigscis.nf
@@ -3,6 +3,7 @@
*/
process COOLTOOLS_EIGSCIS {
+ tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377" : null)
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index 0d7f8be3108b7ddf2f4424fbc3e16b9c6958542d..6557b980d0c586c9168f7ca89eb0e646a2cbee90 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -2,7 +2,8 @@
* Cooltools - diamond-insulation
*/
-process COOLER_INSULATION {
+process COOLTOOLS_INSULATION {
+ tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::cooltools=0.5.1" : null)
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index 4c7d05f40a4d5cfb486b6ea3748f668d2e88398a..86e9e3382e86910f3ad35eae876196e5f01f6928 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
@@ -1,8 +1,9 @@
/*
- * hicexplorer - hicPlotDistVsCounts
+ * hicexplorer - Genomic distance/counts plots
*/
process HIC_PLOT_DIST_VS_COUNTS {
+ tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index 055db6a3045dee93da371bdc2e2bbb0f8df65cae..7b6b6a4bb904dba3facd83755e79841007ece47d 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -8,11 +8,11 @@ process GET_RESTRICTION_FRAGMENTS {
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
- path fasta
+ tuple val(meta), path(fasta)
val(res_site)
output:
- path "*.bed", emit: results
+ tuple val(meta), path("*.bed"), emit: results
path("versions.yml"), emit: versions
script:
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index 2709cdee3530c26820708ef9fd341c424ea14b9a..4fef34d81abb89f4b325f67fe472f6c500a0acbc 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -9,7 +9,7 @@ process GET_VALID_INTERACTION {
input:
tuple val(meta), path(bam)
- path(resfrag)
+ tuple val(meta2), path(resfrag)
output:
tuple val(meta), path("*.validPairs"), emit:valid_pairs
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index aa475c23e150be45e0166ee21103750e5c0f66d6..08222af13c320a28b3ce082f01dc6020a612f3e8 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
+ tuple val(meta2), path(chrsize)
output:
tuple val(meta), path("*.pairs.gz"), path("*.pairs.gz.px2"), emit: pairs
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
deleted file mode 100644
index 68f66bea74a65319549b9834af05cc9a38a1f30a..0000000000000000000000000000000000000000
--- a/modules/nf-core/multiqc/main.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-process MULTIQC {
- label 'process_single'
-
- conda "bioconda::multiqc=1.13"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
-
- input:
- path multiqc_files, stageAs: "?/*"
- path(multiqc_config)
- path(extra_multiqc_config)
- path(multiqc_logo)
-
- output:
- path "*multiqc_report.html", emit: report
- path "*_data" , emit: data
- path "*_plots" , optional:true, emit: plots
- path "versions.yml" , emit: versions
-
- when:
- task.ext.when == null || task.ext.when
-
- script:
- def args = task.ext.args ?: ''
- def config = multiqc_config ? "--config $multiqc_config" : ''
- def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
- """
- multiqc \\
- --force \\
- $args \\
- $config \\
- $extra_config \\
- .
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
- END_VERSIONS
- """
-
- stub:
- """
- touch multiqc_data
- touch multiqc_plots
- touch multiqc_report.html
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
- END_VERSIONS
- """
-}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
deleted file mode 100644
index ebc29b279d565eb11d8923de0b87fd2fb14b1cbe..0000000000000000000000000000000000000000
--- a/modules/nf-core/multiqc/meta.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-name: MultiQC
-description: Aggregate results from bioinformatics analyses across many samples into a single report
-keywords:
- - QC
- - bioinformatics tools
- - Beautiful stand-alone HTML report
-tools:
- - multiqc:
- description: |
- MultiQC searches a given directory for analysis logs and compiles a HTML report.
- It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
- homepage: https://multiqc.info/
- documentation: https://multiqc.info/docs/
- licence: ["GPL-3.0-or-later"]
-
-input:
- - multiqc_files:
- type: file
- description: |
- List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
- - multiqc_config:
- type: file
- description: Optional config yml for MultiQC
- pattern: "*.{yml,yaml}"
- - extra_multiqc_config:
- type: file
- description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
- pattern: "*.{yml,yaml}"
- - multiqc_logo:
- type: file
- description: Optional logo file for MultiQC
- pattern: "*.{png}"
-
-output:
- - report:
- type: file
- description: MultiQC report file
- pattern: "multiqc_report.html"
- - data:
- type: dir
- description: MultiQC data dir
- pattern: "multiqc_data"
- - plots:
- type: file
- description: Plots created by MultiQC
- pattern: "*_data"
- - versions:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
-authors:
- - "@abhi18av"
- - "@bunop"
- - "@drpatelh"
- - "@jfy133"
diff --git a/subworkflows/local/compartments.nf b/subworkflows/local/compartments.nf
index 23d78ac0f3083a00224b130655d94070b1478228..fee68a5d5d8c3a061d02a6f698aff80186b8d7c3 100644
--- a/subworkflows/local/compartments.nf
+++ b/subworkflows/local/compartments.nf
@@ -1,4 +1,4 @@
-include { CALL_COMPARTMENTS } from '../../modules/local/cooltools/eigs-cis'
+include { COOLTOOLS_EIGSCIS } from '../../modules/local/cooltools/eigscis'
workflow COMPARTMENTS {
@@ -10,14 +10,14 @@ workflow COMPARTMENTS {
main:
ch_versions = Channel.empty()
- CALL_COMPARTMENTS (
+ COOLTOOLS_EIGSCIS(
cool,
- fasta.collect(),
- chrsize.collect()
+ fasta.map{it -> it[1]}.collect(),
+ chrsize.map{it -> it[1]}.collect()
)
- ch_versions = ch_versions.mix(CALL_COMPARTMENTS.out.versions)
+ ch_versions = ch_versions.mix(COOLTOOLS_EIGSCIS.out.versions)
emit:
versions = ch_versions
- compartments = CALL_COMPARTMENTS.out.results
+ compartments = COOLTOOLS_EIGSCIS.out.results
}
\ No newline at end of file
diff --git a/subworkflows/local/cooler.nf b/subworkflows/local/cooler.nf
index 7ce15de2065780d12154f1b9fa31044f33948c91..02f5945cf9a2711c9ef2d379b00b161638054f47 100644
--- a/subworkflows/local/cooler.nf
+++ b/subworkflows/local/cooler.nf
@@ -4,12 +4,11 @@
* OUTPUT : cooler files
*/
-include { COOLER_ZOOMIFY } from '../../modules/nf-core/modules/cooler/zoomify/main'
-
-include { COOLER_DUMP } from '../../modules/local/cooler/dump'
-include { COOLER_CLOAD } from '../../modules/local/cooler/cload'
-include { COOLER_BALANCE } from '../../modules/local/cooler/balance'
-include { COOLER_MAKEBINS } from '../../modules/local/cooler/makebins'
+include { COOLER_ZOOMIFY } from '../../modules/nf-core/cooler/zoomify/main'
+include { COOLER_DUMP } from '../../modules/nf-core/cooler/dump/main'
+include { COOLER_CLOAD } from '../../modules/nf-core/cooler/cload/main'
+include { COOLER_BALANCE } from '../../modules/nf-core/cooler/balance/main'
+include { COOLER_MAKEBINS } from '../../modules/nf-core/cooler/makebins/main'
include { SPLIT_COOLER_DUMP } from '../../modules/local/split_cooler_dump'
@@ -25,7 +24,7 @@ workflow COOLER {
take:
pairs // [meta, pairs, index]
- chromsize
+ chromsize // [meta, chromsize]
cool_bins
main:
@@ -34,6 +33,8 @@ workflow COOLER {
//*****************************************
// EXPORT BINS
+ chromsize.combine(cool_bins).view()
+
COOLER_MAKEBINS(
chromsize.combine(cool_bins)
)
@@ -45,7 +46,7 @@ workflow COOLER {
COOLER_CLOAD(
pairs.combine(cool_bins),
- chromsize.collect()
+ chromsize.map{it -> it[1]}.collect()
)
ch_versions = ch_versions.mix(COOLER_CLOAD.out.versions)
@@ -86,10 +87,6 @@ workflow COOLER {
)
ch_versions = ch_versions.mix(COOLER_DUMP.out.versions)
- //COOLER_DUMP(
- // COOLER_ZOOMIFY.out.mcool.combine(cool_bins).map{it->[it[0], it[1], it[2]]}
- //)
-
SPLIT_COOLER_DUMP(
COOLER_DUMP.out.bedpe
)
diff --git a/subworkflows/local/hicpro_mapping.nf b/subworkflows/local/hicpro_mapping.nf
index 3529f4ef247b5d9ad76d48a021e0023a8a948061..a5d31bd07b2a84f8a28d0f01b1b78adbfe20aefc 100644
--- a/subworkflows/local/hicpro_mapping.nf
+++ b/subworkflows/local/hicpro_mapping.nf
@@ -3,9 +3,9 @@
* From the raw sequencing reads to a paired-end bam file
*/
-include { BOWTIE2_ALIGN } from '../../modules/nf-core/modules/bowtie2/align/main'
+include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main'
include { TRIM_READS } from '../../modules/local/hicpro/trim_reads'
-include { BOWTIE2_ALIGN as BOWTIE2_ALIGN_TRIMMED } from '../../modules/nf-core/modules/bowtie2/align/main'
+include { BOWTIE2_ALIGN as BOWTIE2_ALIGN_TRIMMED } from '../../modules/nf-core/bowtie2/align/main'
include { MERGE_BOWTIE2 } from '../../modules/local/hicpro/bowtie2_merge'
include { COMBINE_MATES} from '../../modules/local/hicpro/combine_mates'
include { MAPPING_STATS_DNASE } from '../../modules/local/hicpro/dnase_mapping_stats'
@@ -35,7 +35,7 @@ workflow HICPRO_MAPPING {
take:
reads // [meta, read1, read2]
- index // path
+ index // [meta, path]
ligation_site // value
main:
@@ -50,7 +50,8 @@ workflow HICPRO_MAPPING {
BOWTIE2_ALIGN(
ch_reads,
index.collect(),
- Channel.value(true).collect()
+ true,
+ false
)
ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions)
@@ -66,7 +67,8 @@ workflow HICPRO_MAPPING {
BOWTIE2_ALIGN_TRIMMED(
TRIM_READS.out.fastq,
index.collect(),
- Channel.value(false).collect()
+ false,
+ false
)
ch_versions = ch_versions.mix(BOWTIE2_ALIGN_TRIMMED.out.versions)
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index dd9dd291d864e66122e247f13e516f212ef445bb..a4a2399303570928d763612bd03d88bd4b485f3b 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -2,8 +2,8 @@
* Prepare Annotation Genome for Hi-C data analysis
*/
-include { BOWTIE2_BUILD } from '../../modules/nf-core/modules/bowtie2/build/main'
-include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/modules/custom/getchromsizes/main'
+include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
+include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main'
include { GET_RESTRICTION_FRAGMENTS } from '../../modules/local/hicpro/get_restriction_fragments'
workflow PREPARE_GENOME {
@@ -25,6 +25,7 @@ workflow PREPARE_GENOME {
ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions)
}else{
Channel.fromPath( params.bwt2_index , checkIfExists: true)
+ .map { it -> [[:], it]}
.ifEmpty { exit 1, "Genome index: Provided index not found: ${params.bwt2_index}" }
.set { ch_index }
}
@@ -39,6 +40,7 @@ workflow PREPARE_GENOME {
ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
}else{
Channel.fromPath( params.chromosome_size , checkIfExists: true)
+ .map { it -> [[:], it]}
.set {ch_chromsize}
}
@@ -53,6 +55,7 @@ workflow PREPARE_GENOME {
ch_versions = ch_versions.mix(GET_RESTRICTION_FRAGMENTS.out.versions)
}else if (!params.dnase){
Channel.fromPath( params.restriction_fragments, checkIfExists: true )
+ .map{ it -> [[:], it] }
.set {ch_resfrag}
}else{
ch_resfrag = Channel.empty()
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 3080227c58b6798fac494b0eddd9fe5695782e53..d5ba119a27e94424d993fd1082746fed62566214 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -131,9 +131,19 @@ include { TADS } from '../subworkflows/local/tads'
// MODULE: Installed directly from nf-core/modules
//
include { FASTQC } from '../modules/nf-core/fastqc/main'
-include { MULTIQC } from '../modules/nf-core/multiqc/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ CHANNELS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+Channel.fromPath( params.fasta )
+ .ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
+ .map{it->[[:],it]}
+ .set { ch_fasta }
+
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW