[LINT] fix

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))_.
 

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)
         }
     }

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'"

modules.json

@@ -23,4 +23,4 @@
             }
         }
     }
-}
+}
\ No newline at end of file

modules/nf-core/modules/multiqc/main.nf

-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
-    """
-}

modules/nf-core/modules/multiqc/meta.yml

-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"

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

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"
         }
     ]
-}
+ }