diff --git a/README.md b/README.md
index 7c6a3645fe39fd101c7f5a07dbbf46f312d69dd5..12b1e482024663a957e4eb687a01ad697af86296 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
## Quick Start
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
index c6945ae2c9956f80f02d4d956b0a9d4f304c3c0f..be8324b62b86f8dbdef3dcea81c4dda7206aa508 100755
--- a/lib/WorkflowHic.groovy
+++ b/lib/WorkflowHic.groovy
@@ -56,19 +56,11 @@ class WorkflowHic {
//
private static void genomeExistsError(params, log) {
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-<<<<<<< HEAD
- log.error "=============================================================================\n" +
- " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
- " Currently, the available genome keys are:\n" +
- " ${params.genomes.keySet().join(", ")}\n" +
- "==================================================================================="
-=======
log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
" Currently, the available genome keys are:\n" +
" ${params.genomes.keySet().join(", ")}\n" +
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
->>>>>>> TEMPLATE
System.exit(1)
}
}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index cafb54c35236256cfd15b259782498b839a340ed..fd70920b4cc9807708cac168f754d1ae661ab073 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -60,12 +60,9 @@ class WorkflowMain {
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
-<<<<<<< HEAD
-=======
// Check that a -profile or Nextflow config has been provided to run the pipeline
NfcoreTemplate.checkConfigProvided(workflow, log)
->>>>>>> TEMPLATE
// Check that conda channels are set-up correctly
if (params.enable_conda) {
Utils.checkCondaChannels(log)
@@ -74,12 +71,6 @@ class WorkflowMain {
// Check AWS batch settings
NfcoreTemplate.awsBatch(workflow, params)
-<<<<<<< HEAD
- // Check the hostnames against configured profiles
- NfcoreTemplate.hostName(workflow, params, log)
-
-=======
->>>>>>> TEMPLATE
// Check input has been provided
if (!params.input) {
log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
diff --git a/modules.json b/modules.json
index 4a090fd6e6f1a31b03ba0a8e2fbe9ea1f2633747..53a88ac19cc1c065bb8d6d2f1b1b29040d5ddc44 100644
--- a/modules.json
+++ b/modules.json
@@ -23,4 +23,4 @@
}
}
}
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf
deleted file mode 100644
index 1264aac1ebfc902ae6633862472b412cd929656a..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/multiqc/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-process MULTIQC {
- label 'process_medium'
-
- conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
-
- input:
- path multiqc_files
-
- 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 ?: ''
- """
- multiqc -f $args .
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
- END_VERSIONS
- """
-}
diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml
deleted file mode 100644
index 6fa891efc2c607fa6e1d081171b1bf2a710443ab..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/multiqc/meta.yml
+++ /dev/null
@@ -1,40 +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
-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"
diff --git a/nextflow.config b/nextflow.config
index edcb3878a573997467f9964f645479fe8aecf62f..2a010be8d32879513280943f75f3a54a11555fd0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,14 +10,14 @@
params {
// Input options
- input = null
+ input = null
// References
- genome = null
- igenomes_base = 's3://ngi-igenomes/igenomes'
- igenomes_ignore = false
- chromosome_size = false
- restriction_fragments = false
+ genome = null
+ igenomes_base = 's3://ngi-igenomes/igenomes'
+ igenomes_ignore = false
+ chromosome_size = null
+ restriction_fragments = null
save_reference = false
// Mapping
@@ -32,7 +32,7 @@ params {
min_mapq = 10
// Digestion Hi-C
- digestion = false
+ digestion = null
ligation_site = null
restriction_site = null
digest {
@@ -67,7 +67,7 @@ params {
// Contact maps
save_raw_maps = false
bin_size = '1000000'
- res_zoomify = false
+ res_zoomify = null
hicpro_maps = false
ice_max_iter = 100
ice_filter_low_count_perc = 0.02
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ad0cab5329262ca66476703c6f93ca0ca441a811..9aa880757ed6ecc8d684371152194ab365f7ba8f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -93,27 +93,29 @@
"properties": {
"digestion": {
"type": "string",
- "default": "hindiii",
- "description": "Name of restriction enzyme to automatically set the restriction_site and ligation_site options"
+ "default": null,
+ "description": "Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)"
},
"restriction_site": {
"type": "string",
- "default": "'A^AGCTT'",
+ "default": null,
"description": "Restriction motifs used during digestion. Several motifs (comma separated) can be provided."
},
"ligation_site": {
"type": "string",
- "default": "'AAGCTAGCTT",
+ "default": null,
"description": "Expected motif after DNA ligation. Several motifs (comma separated) can be provided."
},
"chromosome_size": {
"type": "string",
+ "format": "file-path",
"description": "Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.",
"fa_icon": "far fa-file-alt",
"help_text": "If not specified, the pipeline will build this file from the reference genome file"
},
"restriction_fragments": {
"type": "string",
+ "format": "file-path",
"description": "Full path to restriction fragment (bed) file.",
"fa_icon": "far fa-file-alt",
"help_text": "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option"
@@ -214,9 +216,13 @@
"save_interaction_bam": {
"type": "boolean",
"description": "Save a BAM file where all reads are flagged by their interaction classes"
+ },
+ "save_pairs_intermediates": {
+ "type": "boolean",
+ "description": "Save all types of non valid read pairs in distinct output files"
}
}
- },
+ },
"contact_maps": {
"title": "Contact maps",
"type": "object",
@@ -257,7 +263,11 @@
"type": "string",
"default": "5000",
"description": "Maximum resolution to build mcool file"
- }
+ },
+ "save_raw_maps": {
+ "type": "boolean",
+ "description": "Save raw contact maps"
+ }
}
},
"downstream_analysis": {
@@ -311,7 +321,7 @@
"description": "Do not run TADs calling"
},
"skip_compartments": {
- "type": "string",
+ "type": "boolean",
"description": "Do not run compartments calling"
},
"skip_balancing": {
@@ -527,6 +537,7 @@
{
"$ref": "#/definitions/generic_options"
},
+ {
"$ref": "#/definitions/institutional_config_options"
},
{
@@ -536,4 +547,4 @@
"$ref": "#/definitions/generic_options"
}
]
-}
+ }