Initial template commit

conf/base.config

+/*
+ * -------------------------------------------------
+ *  nf-core/hic Nextflow base config file
+ * -------------------------------------------------
+ * A 'blank slate' config file, appropriate for general
+ * use on most high performace compute environments.
+ * Assumes that all software is installed and available
+ * on the PATH. Runs in `local` mode - all jobs will be
+ * run on the logged in environment.
+ */
+
+process {
+
+  // TODO nf-core: Check the defaults for all processes
+  cpus = { check_max( 1 * task.attempt, 'cpus' ) }
+  memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+  time = { check_max( 2.h * task.attempt, 'time' ) }
+
+  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+  maxRetries = 1
+  maxErrors = '-1'
+
+  // Process-specific resource requirements
+  // TODO nf-core: Customise requirements for specific processes.
+  // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+}
+
+params {
+  // Defaults only, expecting to be overwritten
+  max_memory = 128.GB
+  max_cpus = 16
+  max_time = 240.h
+  igenomes_base = 's3://ngi-igenomes/igenomes/'
+}

conf/igenomes.config

+/*
+ * -------------------------------------------------
+ *  Nextflow config file for iGenomes paths
+ * -------------------------------------------------
+ * Defines reference genomes, using iGenome paths
+ * Can be used by any config that customises the base
+ * path using $params.igenomes_base / --igenomes_base
+ */
+
+params {
+  // illumina iGenomes reference file paths
+  // TODO nf-core: Add new reference types and strip out those that are not needed
+  genomes {
+    'GRCh37' {
+      bed12   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
+    }
+    'GRCm38' {
+      bed12   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
+    }
+    'TAIR10' {
+      bed12   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
+    }
+    'EB2' {
+      bed12   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
+    }
+    'UMD3.1' {
+      bed12   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
+    }
+    'WBcel235' {
+      bed12   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
+    }
+    'CanFam3.1' {
+      bed12   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
+    }
+    'GRCz10' {
+      bed12   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
+    }
+    'BDGP6' {
+      bed12   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
+    }
+    'EquCab2' {
+      bed12   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
+    }
+    'EB1' {
+      bed12   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
+    }
+    'Galgal4' {
+      bed12   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
+    }
+    'Gm01' {
+      bed12   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
+    }
+    'Mmul_1' {
+      bed12   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
+    }
+    'IRGSP-1.0' {
+      bed12   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
+    }
+    'CHIMP2.1.4' {
+      bed12   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
+    }
+    'Rnor_6.0' {
+      bed12   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
+    }
+    'R64-1-1' {
+      bed12   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
+    }
+    'EF2' {
+      bed12   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
+    }
+    'Sbi1' {
+      bed12   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
+    }
+    'Sscrofa10.2' {
+      bed12   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
+    }
+    'AGPv3' {
+      bed12   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
+      fasta   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
+      gtf     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
+      star    = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
+    }
+  }
+}

conf/test.config

+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/hic -profile test
+ */
+
+params {
+  config_profile_name = 'Test profile'
+  config_profile_description = 'Minimal test dataset to check pipeline function'
+  // Limit resources so that this can run on Travis
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+  // Input data
+  // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+  // TODO nf-core: Give any required params for the test so that command line flags are not needed
+  singleEnd = false
+  readPaths = [
+    ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']],
+    ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']]
+  ]
+}

docs/README.md

+# nf-core/hic: Documentation
+
+The nf-core/hic documentation is split into the following files:
+
+1. [Installation](https://nf-co.re/usage/installation)
+2. Pipeline configuration
+    * [Local installation](https://nf-co.re/usage/local_installation)
+    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
+3. [Running the pipeline](usage.md)
+4. [Output and how to interpret the results](output.md)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)

docs/output.md

+# nf-core/hic: Output
+
+This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
+
+<!-- TODO nf-core: Write this documentation describing your workflow's output -->
+
+## Pipeline overview
+The pipeline is built using [Nextflow](https://www.nextflow.io/)
+and processes data using the following steps:
+
+* [FastQC](#fastqc) - read quality control
+* [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
+
+## FastQC
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%T/A/G/C). You get information about adapter contamination and other overrepresented sequences.
+
+For further reading and documentation see the [FastQC help](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+
+> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. To see how your reads look after trimming, look at the FastQC reports in the `trim_galore` directory.
+
+**Output directory: `results/fastqc`**
+
+* `sample_fastqc.html`
+  * FastQC report, containing quality metrics for your untrimmed raw fastq files
+* `zips/sample_fastqc.zip`
+  * zip file containing the FastQC report, tab-delimited data file and plot images
+
+
+## MultiQC
+[MultiQC](http://multiqc.info) is a visualisation tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in within the report data directory.
+
+The pipeline has special steps which allow the software versions used to be reported in the MultiQC output for future traceability.
+
+**Output directory: `results/multiqc`**
+
+* `Project_multiqc_report.html`
+  * MultiQC report - a standalone HTML file that can be viewed in your web browser
+* `Project_multiqc_data/`
+  * Directory containing parsed statistics from the different tools used in the pipeline
+
+For more information about how to use MultiQC reports, see [http://multiqc.info](http://multiqc.info)

docs/usage.md

+# nf-core/hic: Usage
+
+## Table of contents
+
+<!-- Install Atom plugin markdown-toc-auto for this ToC to auto-update on save -->
+<!-- TOC START min:2 max:3 link:true asterisk:true update:true -->
+* [Table of contents](#table-of-contents)
+* [Introduction](#introduction)
+* [Running the pipeline](#running-the-pipeline)
+  * [Updating the pipeline](#updating-the-pipeline)
+  * [Reproducibility](#reproducibility)
+* [Main arguments](#main-arguments)
+  * [`-profile`](#-profile)
+  * [`--reads`](#--reads)
+  * [`--singleEnd`](#--singleend)
+* [Reference genomes](#reference-genomes)
+  * [`--genome` (using iGenomes)](#--genome-using-igenomes)
+  * [`--fasta`](#--fasta)
+  * [`--igenomesIgnore`](#--igenomesignore)
+* [Job resources](#job-resources)
+  * [Automatic resubmission](#automatic-resubmission)
+  * [Custom resource requests](#custom-resource-requests)
+* [AWS Batch specific parameters](#aws-batch-specific-parameters)
+  * [`--awsqueue`](#--awsqueue)
+  * [`--awsregion`](#--awsregion)
+* [Other command line parameters](#other-command-line-parameters)
+  * [`--outdir`](#--outdir)
+  * [`--email`](#--email)
+  * [`-name`](#-name)
+  * [`-resume`](#-resume)
+  * [`-c`](#-c)
+  * [`--custom_config_version`](#--custom_config_version)
+  * [`--custom_config_base`](#--custom_config_base)
+  * [`--max_memory`](#--max_memory)
+  * [`--max_time`](#--max_time)
+  * [`--max_cpus`](#--max_cpus)
+  * [`--plaintext_email`](#--plaintext_email)
+  * [`--monochrome_logs`](#--monochrome_logs)
+  * [`--multiqc_config`](#--multiqc_config)
+<!-- TOC END -->
+
+
+## Introduction
+Nextflow handles job submissions on SLURM or other environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through `screen` / `tmux` or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.
+
+It is recommended to limit the Nextflow Java virtual machines memory. We recommend adding the following line to your environment (typically in `~/.bashrc` or `~./bash_profile`):
+
+```bash
+NXF_OPTS='-Xms1g -Xmx4g'
+```
+
+<!-- TODO nf-core: Document required command line parameters to run the pipeline-->
+
+## Running the pipeline
+The typical command for running the pipeline is as follows:
+
+```bash
+nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile docker
+```
+
+This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
+
+Note that the pipeline will create the following files in your working directory:
+
+```bash
+work            # Directory containing the nextflow working files
+results         # Finished results (configurable, see below)
+.nextflow_log   # Log file from Nextflow
+# Other nextflow hidden files, eg. history of pipeline runs and old logs.
+```
+
+### Updating the pipeline
+When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
+
+```bash
+nextflow pull nf-core/hic
+```
+
+### Reproducibility
+It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+
+First, go to the [nf-core/hic releases page](https://github.com/nf-core/hic/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
+
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
+
+
+## Main arguments
+
+### `-profile`
+Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. Note that multiple profiles can be loaded, for example: `-profile docker` - the order of arguments is important!
+
+If `-profile` is not specified at all the pipeline will be run locally and expects all software to be installed and available on the `PATH`.
+
+* `awsbatch`
+  * A generic configuration profile to be used with AWS Batch.
+* `conda`
+  * A generic configuration profile to be used with [conda](https://conda.io/docs/)
+  * Pulls most software from [Bioconda](https://bioconda.github.io/)
+* `docker`
+  * A generic configuration profile to be used with [Docker](http://docker.com/)
+  * Pulls software from dockerhub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/)
+* `singularity`
+  * A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/)
+  * Pulls software from DockerHub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/)
+* `test`
+  * A profile with a complete configuration for automated testing
+  * Includes links to test data so needs no other parameters
+
+<!-- TODO nf-core: Document required command line parameters -->
+
+### `--reads`
+Use this to specify the location of your input FastQ files. For example:
+
+```bash
+--reads 'path/to/data/sample_*_{1,2}.fastq'
+```
+
+Please note the following requirements:
+
+1. The path must be enclosed in quotes
+2. The path must have at least one `*` wildcard character
+3. When using the pipeline with paired end data, the path must use `{1,2}` notation to specify read pairs.
+
+If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
+
+### `--singleEnd`
+By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--singleEnd` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
+
+```bash
+--singleEnd --reads '*.fastq'
+```
+
+It is not possible to run a mixture of single-end and paired-end files in one run.
+
+
+## Reference genomes
+
+The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.
+
+### `--genome` (using iGenomes)
+There are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.
+
+You can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:
+
+* Human
+  * `--genome GRCh37`
+* Mouse
+  * `--genome GRCm38`
+* _Drosophila_
+  * `--genome BDGP6`
+* _S. cerevisiae_
+  * `--genome 'R64-1-1'`
+
+> There are numerous others - check the config file for more.
+
+Note that you can use the same configuration setup to save sets of reference files for your own use, even if they are not part of the iGenomes resource. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for instructions on where to save such a file.
+
+The syntax for this reference configuration is as follows:
+
+<!-- TODO nf-core: Update reference genome example according to what is needed -->
+
+```nextflow
+params {
+  genomes {
+    'GRCh37' {
+      fasta   = '<path to the genome fasta file>' // Used if no star index given
+    }
+    // Any number of additional genomes, key is used with --genome
+  }
+}
+```
+
+<!-- TODO nf-core: Describe reference path flags -->
+### `--fasta`
+If you prefer, you can specify the full path to your reference genome when you run the pipeline:
+
+```bash
+--fasta '[path to Fasta reference]'
+```
+
+### `--igenomesIgnore`
+Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
+
+## Job resources
+### Automatic resubmission
+Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.
+
+### Custom resource requests
+Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files hosted at [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
+
+If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
+
+If you have any questions or issues please send us a message on [Slack](https://nf-core-invite.herokuapp.com/).
+
+## AWS Batch specific parameters
+Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration. Please use the `-awsbatch` profile and then specify all of the following parameters.
+### `--awsqueue`
+The JobQueue that you intend to use on AWS Batch.
+### `--awsregion`
+The AWS region to run your job in. Default is set to `eu-west-1` but can be adjusted to your needs.
+
+Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a S3 storage bucket of your choice - you'll get an error message notifying you if you didn't.
+
+## Other command line parameters
+
+<!-- TODO nf-core: Describe any other command line flags here -->
+
+### `--outdir`
+The output directory where the results will be saved.
+
+### `--email`
+Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
+
+### `-name`
+Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+
+This is used in the MultiQC report (if not default) and in the summary HTML / e-mail (always).
+
+**NB:** Single hyphen (core Nextflow option)
+
+### `-resume`
+Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.
+
+You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
+
+**NB:** Single hyphen (core Nextflow option)
+
+### `-c`
+Specify the path to a specific config file (this is a core NextFlow command).
+
+**NB:** Single hyphen (core Nextflow option)
+
+Note - you can use this to override pipeline defaults.
+
+### `--custom_config_version`
+Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.
+
+```bash
+## Download and use config file with following git commid id
+--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
+```
+
+### `--custom_config_base`
+If you're running offline, nextflow will not be able to fetch the institutional config files
+from the internet. If you don't need them, then this is not a problem. If you do need them,
+you should download the files from the repo and tell nextflow where to find them with the
+`custom_config_base` option. For example:
+
+```bash
+## Download and unzip the config files
+cd /path/to/my/configs
+wget https://github.com/nf-core/configs/archive/master.zip
+unzip master.zip
+
+## Run the pipeline
+cd /path/to/my/data
+nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
+```
+
+> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
+> files + singularity containers + institutional configs in one go for you, to make this process easier.
+
+### `--max_memory`
+Use to set a top-limit for the default memory requirement for each process.
+Should be a string in the format integer-unit. eg. `--max_memory '8.GB'`
+
+### `--max_time`
+Use to set a top-limit for the default time requirement for each process.
+Should be a string in the format integer-unit. eg. `--max_time '2.h'`
+
+### `--max_cpus`
+Use to set a top-limit for the default CPU requirement for each process.
+Should be a string in the format integer-unit. eg. `--max_cpus 1`
+
+### `--plaintext_email`
+Set to receive plain-text e-mails instead of HTML formatted.
+
+### `--monochrome_logs`
+Set to disable colourful command line output and live life in monochrome.
+
+### `--multiqc_config`
+Specify a path to a custom MultiQC configuration file.

environment.yml

+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nf-core-hic-1.0dev
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  # TODO nf-core: Add required software dependencies here
+  - fastqc=0.11.8
+  - multiqc=1.7

main.nf

+#!/usr/bin/env nextflow
+/*
+========================================================================================
+                         nf-core/hic
+========================================================================================
+ nf-core/hic Analysis Pipeline.
+ #### Homepage / Documentation
+ https://github.com/nf-core/hic
+----------------------------------------------------------------------------------------
+*/
+
+
+def helpMessage() {
+    // TODO nf-core: Add to this help message with new command line parameters
+    log.info nfcoreHeader()
+    log.info"""
+
+    Usage:
+
+    The typical command for running the pipeline is as follows:
+
+    nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile docker
+
+    Mandatory arguments:
+      --reads                       Path to input data (must be surrounded with quotes)
+      -profile                      Configuration profile to use. Can use multiple (comma separated)
+                                    Available: conda, docker, singularity, awsbatch, test and more.
+
+    Options:
+      --genome                      Name of iGenomes reference
+      --singleEnd                   Specifies that the input is single end reads
+
+    References                      If not specified in the configuration file or you wish to overwrite any of the references.
+      --fasta                       Path to Fasta reference
+
+    Other options:
+      --outdir                      The output directory where the results will be saved
+      --email                       Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
+      --maxMultiqcEmailFileSize     Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
+      -name                         Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+
+    AWSBatch options:
+      --awsqueue                    The AWSBatch JobQueue that needs to be set when running on AWSBatch
+      --awsregion                   The AWS Region for your AWS Batch job to run on
+    """.stripIndent()
+}
+
+/*
+ * SET UP CONFIGURATION VARIABLES
+ */
+
+// Show help emssage
+if (params.help){
+    helpMessage()
+    exit 0
+}
+
+// Check if genome exists in the config file
+if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+    exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
+}
+
+// TODO nf-core: Add any reference files that are needed
+// Configurable reference genomes
+fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
+if ( params.fasta ){
+    fasta = file(params.fasta)
+    if( !fasta.exists() ) exit 1, "Fasta file not found: ${params.fasta}"
+}
+//
+// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
+// If you want to use the above in a process, define the following:
+//   input:
+//   file fasta from fasta
+//
+
+
+// Has the run name been specified by the user?
+//  this has the bonus effect of catching both -name and --name
+custom_runName = params.name
+if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
+  custom_runName = workflow.runName
+}
+
+
+if( workflow.profile == 'awsbatch') {
+  // AWSBatch sanity checking
+  if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
+  // Check outdir paths to be S3 buckets if running on AWSBatch
+  // related: https://github.com/nextflow-io/nextflow/issues/813
+  if (!params.outdir.startsWith('s3:')) exit 1, "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
+  // Prevent trace files to be stored on S3 since S3 does not support rolling files.
+  if (workflow.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
+}
+
+// Stage config files
+ch_multiqc_config = Channel.fromPath(params.multiqc_config)
+ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
+
+/*
+ * Create a channel for input read files
+ */
+if(params.readPaths){
+    if(params.singleEnd){
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [file(row[1][0])]] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .into { read_files_fastqc; read_files_trimming }
+    } else {
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .into { read_files_fastqc; read_files_trimming }
+    }
+} else {
+    Channel
+        .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
+        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --singleEnd on the command line." }
+        .into { read_files_fastqc; read_files_trimming }
+}
+
+
+// Header log info
+log.info nfcoreHeader()
+def summary = [:]
+if(workflow.revision) summary['Pipeline Release'] = workflow.revision
+summary['Run Name']         = custom_runName ?: workflow.runName
+// TODO nf-core: Report custom parameters here
+summary['Reads']            = params.reads
+summary['Fasta Ref']        = params.fasta
+summary['Data Type']        = params.singleEnd ? 'Single-End' : 'Paired-End'
+summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
+if(workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
+summary['Output dir']       = params.outdir
+summary['Launch dir']       = workflow.launchDir
+summary['Working dir']      = workflow.workDir
+summary['Script dir']       = workflow.projectDir
+summary['User']             = workflow.userName
+if(workflow.profile == 'awsbatch'){
+   summary['AWS Region']    = params.awsregion
+   summary['AWS Queue']     = params.awsqueue
+}
+summary['Config Profile'] = workflow.profile
+if(params.config_profile_description) summary['Config Description'] = params.config_profile_description
+if(params.config_profile_contact)     summary['Config Contact']     = params.config_profile_contact
+if(params.config_profile_url)         summary['Config URL']         = params.config_profile_url
+if(params.email) {
+  summary['E-mail Address']  = params.email
+  summary['MultiQC maxsize'] = params.maxMultiqcEmailFileSize
+}
+log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
+log.info "\033[2m----------------------------------------------------\033[0m"
+
+// Check the hostnames against configured profiles
+checkHostname()
+
+def create_workflow_summary(summary) {
+    def yaml_file = workDir.resolve('workflow_summary_mqc.yaml')
+    yaml_file.text  = """
+    id: 'nf-core-hic-summary'
+    description: " - this information is collected when the pipeline is started."
+    section_name: 'nf-core/hic Workflow Summary'
+    section_href: 'https://github.com/nf-core/hic'
+    plot_type: 'html'
+    data: |
+        <dl class=\"dl-horizontal\">
+${summary.collect { k,v -> "            <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
+        </dl>
+    """.stripIndent()
+
+   return yaml_file
+}
+
+
+/*
+ * Parse software version numbers
+ */
+process get_software_versions {
+    publishDir "${params.outdir}/pipeline_info", mode: 'copy',
+    saveAs: {filename ->
+        if (filename.indexOf(".csv") > 0) filename
+        else null
+    }
+
+    output:
+    file 'software_versions_mqc.yaml' into software_versions_yaml
+    file "software_versions.csv"
+
+    script:
+    // TODO nf-core: Get all tools to print their version number here
+    """
+    echo $workflow.manifest.version > v_pipeline.txt
+    echo $workflow.nextflow.version > v_nextflow.txt
+    fastqc --version > v_fastqc.txt
+    multiqc --version > v_multiqc.txt
+    scrape_software_versions.py &> software_versions_mqc.yaml
+    """
+}
+
+
+
+/*
+ * STEP 1 - FastQC
+ */
+process fastqc {
+    tag "$name"
+    publishDir "${params.outdir}/fastqc", mode: 'copy',
+        saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
+
+    input:
+    set val(name), file(reads) from read_files_fastqc
+
+    output:
+    file "*_fastqc.{zip,html}" into fastqc_results
+
+    script:
+    """
+    fastqc -q $reads
+    """
+}
+
+
+
+/*
+ * STEP 2 - MultiQC
+ */
+process multiqc {
+    publishDir "${params.outdir}/MultiQC", mode: 'copy'
+
+    input:
+    file multiqc_config from ch_multiqc_config
+    // TODO nf-core: Add in log files from your new processes for MultiQC to find!
+    file ('fastqc/*') from fastqc_results.collect().ifEmpty([])
+    file ('software_versions/*') from software_versions_yaml.collect()
+    file workflow_summary from create_workflow_summary(summary)
+
+    output:
+    file "*multiqc_report.html" into multiqc_report
+    file "*_data"
+    file "multiqc_plots"
+
+    script:
+    rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
+    rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
+    // TODO nf-core: Specify which MultiQC modules to use with -m for a faster run time
+    """
+    multiqc -f $rtitle $rfilename --config $multiqc_config .
+    """
+}
+
+
+
+/*
+ * STEP 3 - Output Description HTML
+ */
+process output_documentation {
+    publishDir "${params.outdir}/pipeline_info", mode: 'copy'
+
+    input:
+    file output_docs from ch_output_docs
+
+    output:
+    file "results_description.html"
+
+    script:
+    """
+    markdown_to_html.r $output_docs results_description.html
+    """
+}
+
+
+
+/*
+ * Completion e-mail notification
+ */
+workflow.onComplete {
+
+    // Set up the e-mail variables
+    def subject = "[nf-core/hic] Successful: $workflow.runName"
+    if(!workflow.success){
+      subject = "[nf-core/hic] FAILED: $workflow.runName"
+    }
+    def email_fields = [:]
+    email_fields['version'] = workflow.manifest.version
+    email_fields['runName'] = custom_runName ?: workflow.runName
+    email_fields['success'] = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration'] = workflow.duration
+    email_fields['exitStatus'] = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport'] = (workflow.errorReport ?: 'None')
+    email_fields['commandLine'] = workflow.commandLine
+    email_fields['projectDir'] = workflow.projectDir
+    email_fields['summary'] = summary
+    email_fields['summary']['Date Started'] = workflow.start
+    email_fields['summary']['Date Completed'] = workflow.complete
+    email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
+    email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
+    if(workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
+    if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
+    if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
+    if(workflow.container) email_fields['summary']['Docker image'] = workflow.container
+    email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
+    email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
+    email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    // TODO nf-core: If not using MultiQC, strip out this code (including params.maxMultiqcEmailFileSize)
+    // On success try attach the multiqc report
+    def mqc_report = null
+    try {
+        if (workflow.success) {
+            mqc_report = multiqc_report.getVal()
+            if (mqc_report.getClass() == ArrayList){
+                log.warn "[nf-core/hic] Found multiple reports from process 'multiqc', will use only one"
+                mqc_report = mqc_report[0]
+            }
+        }
+    } catch (all) {
+        log.warn "[nf-core/hic] Could not attach MultiQC report to summary email"
+    }
+
+    // Render the TXT template
+    def engine = new groovy.text.GStringTemplateEngine()
+    def tf = new File("$baseDir/assets/email_template.txt")
+    def txt_template = engine.createTemplate(tf).make(email_fields)
+    def email_txt = txt_template.toString()
+
+    // Render the HTML template
+    def hf = new File("$baseDir/assets/email_template.html")
+    def html_template = engine.createTemplate(hf).make(email_fields)
+    def email_html = html_template.toString()
+
+    // Render the sendmail template
+    def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.maxMultiqcEmailFileSize.toBytes() ]
+    def sf = new File("$baseDir/assets/sendmail_template.txt")
+    def sendmail_template = engine.createTemplate(sf).make(smail_fields)
+    def sendmail_html = sendmail_template.toString()
+
+    // Send the HTML e-mail
+    if (params.email) {
+        try {
+          if( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') }
+          // Try to send HTML e-mail using sendmail
+          [ 'sendmail', '-t' ].execute() << sendmail_html
+          log.info "[nf-core/hic] Sent summary e-mail to $params.email (sendmail)"
+        } catch (all) {
+          // Catch failures and try with plaintext
+          [ 'mail', '-s', subject, params.email ].execute() << email_txt
+          log.info "[nf-core/hic] Sent summary e-mail to $params.email (mail)"
+        }
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_d = new File( "${params.outdir}/pipeline_info/" )
+    if( !output_d.exists() ) {
+      output_d.mkdirs()
+    }
+    def output_hf = new File( output_d, "pipeline_report.html" )
+    output_hf.withWriter { w -> w << email_html }
+    def output_tf = new File( output_d, "pipeline_report.txt" )
+    output_tf.withWriter { w -> w << email_txt }
+
+    c_reset = params.monochrome_logs ? '' : "\033[0m";
+    c_purple = params.monochrome_logs ? '' : "\033[0;35m";
+    c_green = params.monochrome_logs ? '' : "\033[0;32m";
+    c_red = params.monochrome_logs ? '' : "\033[0;31m";
+
+    if (workflow.stats.ignoredCountFmt > 0 && workflow.success) {
+      log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
+      log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCountFmt} ${c_reset}"
+      log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCountFmt} ${c_reset}"
+    }
+
+    if(workflow.success){
+        log.info "${c_purple}[nf-core/hic]${c_green} Pipeline completed successfully${c_reset}"
+    } else {
+        checkHostname()
+        log.info "${c_purple}[nf-core/hic]${c_red} Pipeline completed with errors${c_reset}"
+    }
+
+}
+
+
+def nfcoreHeader(){
+    // Log colors ANSI codes
+    c_reset = params.monochrome_logs ? '' : "\033[0m";
+    c_dim = params.monochrome_logs ? '' : "\033[2m";
+    c_black = params.monochrome_logs ? '' : "\033[0;30m";
+    c_green = params.monochrome_logs ? '' : "\033[0;32m";
+    c_yellow = params.monochrome_logs ? '' : "\033[0;33m";
+    c_blue = params.monochrome_logs ? '' : "\033[0;34m";
+    c_purple = params.monochrome_logs ? '' : "\033[0;35m";
+    c_cyan = params.monochrome_logs ? '' : "\033[0;36m";
+    c_white = params.monochrome_logs ? '' : "\033[0;37m";
+
+    return """    ${c_dim}----------------------------------------------------${c_reset}
+                                            ${c_green},--.${c_black}/${c_green},-.${c_reset}
+    ${c_blue}        ___     __   __   __   ___     ${c_green}/,-._.--~\'${c_reset}
+    ${c_blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${c_yellow}}  {${c_reset}
+    ${c_blue}  | \\| |       \\__, \\__/ |  \\ |___     ${c_green}\\`-._,-`-,${c_reset}
+                                            ${c_green}`._,._,\'${c_reset}
+    ${c_purple}  nf-core/hic v${workflow.manifest.version}${c_reset}
+    ${c_dim}----------------------------------------------------${c_reset}
+    """.stripIndent()
+}
+
+def checkHostname(){
+    def c_reset = params.monochrome_logs ? '' : "\033[0m"
+    def c_white = params.monochrome_logs ? '' : "\033[0;37m"
+    def c_red = params.monochrome_logs ? '' : "\033[1;91m"
+    def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
+    if(params.hostnames){
+        def hostname = "hostname".execute().text.trim()
+        params.hostnames.each { prof, hnames ->
+            hnames.each { hname ->
+                if(hostname.contains(hname) && !workflow.profile.contains(prof)){
+                    log.error "====================================================\n" +
+                            "  ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
+                            "  but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
+                            "  ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
+                            "============================================================"
+                }
+            }
+        }
+    }
+}

nextflow.config

+/*
+ * -------------------------------------------------
+ *  nf-core/hic Nextflow config file
+ * -------------------------------------------------
+ * Default config options for all environments.
+ */
+
+// Global default params, used in configs
+params {
+
+  // Workflow flags
+  // TODO nf-core: Specify your pipeline's command line flags
+  reads = "data/*{1,2}.fastq.gz"
+  singleEnd = false
+  outdir = './results'
+
+  // Boilerplate options
+  name = false
+  multiqc_config = "$baseDir/assets/multiqc_config.yaml"
+  email = false
+  maxMultiqcEmailFileSize = 25.MB
+  plaintext_email = false
+  monochrome_logs = false
+  help = false
+  igenomes_base = "./iGenomes"
+  tracedir = "${params.outdir}/pipeline_info"
+  awsqueue = false
+  awsregion = 'eu-west-1'
+  igenomesIgnore = false
+  custom_config_version = 'master'
+  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+  hostnames = false
+  config_profile_description = false
+  config_profile_contact = false
+  config_profile_url = false
+}
+
+// Container slug. Stable releases should specify release tag!
+// Developmental code should specify :dev
+process.container = 'nfcore/hic:dev'
+
+// Load base.config by default for all pipelines
+includeConfig 'conf/base.config'
+
+// Load nf-core custom profiles from different Institutions
+try {
+  includeConfig "${params.custom_config_base}/nfcore_custom.config"
+} catch (Exception e) {
+  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
+}
+
+profiles {
+  awsbatch { includeConfig 'conf/awsbatch.config' }
+  conda { process.conda = "$baseDir/environment.yml" }
+  debug { process.beforeScript = 'echo $HOSTNAME' }
+  docker { docker.enabled = true }
+  singularity { singularity.enabled = true }
+  test { includeConfig 'conf/test.config' }
+}
+
+// Load igenomes.config if required
+if(!params.igenomesIgnore){
+  includeConfig 'conf/igenomes.config'
+}
+
+// Capture exit codes from upstream processes when piping
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+
+timeline {
+  enabled = true
+  file = "${params.tracedir}/execution_timeline.html"
+}
+report {
+  enabled = true
+  file = "${params.tracedir}/execution_report.html"
+}
+trace {
+  enabled = true
+  file = "${params.tracedir}/execution_trace.txt"
+}
+dag {
+  enabled = true
+  file = "${params.tracedir}/pipeline_dag.svg"
+}
+
+manifest {
+  name = 'nf-core/hic'
+  author = 'Nicolas Servant'
+  homePage = 'https://github.com/nf-core/hic'
+  description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
+  mainScript = 'main.nf'
+  nextflowVersion = '>=0.32.0'
+  version = '1.0dev'
+}
+
+// Function to ensure that resource requirements don't go beyond
+// a maximum limit
+def check_max(obj, type) {
+  if(type == 'memory'){
+    try {
+      if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+        return params.max_memory as nextflow.util.MemoryUnit
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if(type == 'time'){
+    try {
+      if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+        return params.max_time as nextflow.util.Duration
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if(type == 'cpus'){
+    try {
+      return Math.min( obj, params.max_cpus as int )
+    } catch (all) {
+      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+      return obj
+    }
+  }
+}