Merge pull request #79 from ewels/nf-core-template-merge-1.11

nf-core template merge v1.11

.github/CONTRIBUTING.md

@@ -59,4 +59,4 @@ For further information/help, please consult the [nf-core/hic documentation](htt
 don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel
 ([join our Slack here](https://nf-co.re/join/slack)).
 
-For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/docs) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/usage) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -35,7 +35,7 @@ Steps to reproduce the behaviour:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
 

.github/workflows/awsfulltest.yml

 name: nf-core AWS full size tests
-# This workflow is triggered on push to the master branch.
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   release:
     types: [published]
+  workflow_dispatch:
 
 jobs:
   run-awstest:

.github/workflows/awstest.yml

 name: nf-core AWS test
 # This workflow is triggered on push to the master branch.
-# It runs the -profile 'test' on AWS batch
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
 
 jobs:
   run-awstest:
@@ -36,4 +35,4 @@ jobs:
           --job-name nf-core-hic \
           --job-queue $AWS_JOB_QUEUE \
           --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/ci.yml

@@ -34,13 +34,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/hic:1.2.2
+        run: docker build --no-cache . -t nfcore/hic:dev
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/hic:dev
-          docker tag nfcore/hic:dev nfcore/hic:1.2.2
+          docker tag nfcore/hic:dev nfcore/hic:dev
 
       - name: Install Nextflow
         run: |

CHANGELOG.md

@@ -3,6 +3,11 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.3.0dev
+
+* Template update for nf-core/tools v1.11
+* Minor fix to summary log messages in pipeline header
+
 ## v1.2.2 - 2020-09-02
 
 ### `Added`

Dockerfile

-FROM nfcore/base:1.10.2
-
+FROM nfcore/base:1.11
 LABEL authors="Nicolas Servant" \
       description="Docker image containing all software requirements for the nf-core/hic pipeline"
 
@@ -10,10 +9,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-hic-1.2.2/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.3.0dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.2.2 > nf-core-hic-1.2.2.yml
+RUN conda env export --name nf-core-hic-1.3.0dev > nf-core-hic-1.3.0dev.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

README.md

@@ -42,17 +42,14 @@ sites (bowtie2)
 
 ## Quick Start
 
-i. Install [`nextflow`](https://nf-co.re/usage/installation)
+1. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-ii. Install either [`Docker`](https://docs.docker.com/engine/installation/)
-or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/)
-for full pipeline reproducibility (please only use [`Conda`](https://conda.io/miniconda.html)
-as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))
+2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
-iii. Download the pipeline and test it on a minimal dataset with a single command
+3. Download the pipeline and test it on a minimal dataset with a single command
 
     ```bash
-nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute>
+    nextflow run nf-core/hic -profile test,<docker/singularity/podman/conda/institute>
     ```
 
     > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation)
@@ -61,35 +58,19 @@ If so, you can simply use `-profile <institute>` in your command.
     This will enable either `docker` or `singularity` and set the appropriate execution
     settings for your local compute environment.
 
-iv. Start running your own analysis!
+4. Start running your own analysis!
 
     ```bash
-nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
+    nextflow run nf-core/hic -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
     ```
 
-See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running
-the pipeline.
+See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running the pipeline.
 
 ## Documentation
 
-The nf-core/hic pipeline comes with documentation about the pipeline,
-found in the `docs/` directory:
+The nf-core/hic pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/hic/usage) and [output](https://nf-co.re/hic/output).
 
-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](docs/usage.md)
-4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
-
-The nf-core/hic pipeline comes with documentation about the pipeline which
-you can read at [https://nf-co.re/hic/usage](https://nf-co.re/hic/usage) or
-find in the [`docs/` directory](docs).
-
-For further information or help, don't hesitate to get in touch on
-[Slack](https://nfcore.slack.com/channels/hic).
+For further information or help, don't hesitate to get in touch on [Slack](https://nfcore.slack.com/channels/hic).
 You can join with [this invite](https://nf-co.re/join/slack).
 
 ## Credits

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.
+## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/hic/output](https://nf-co.re/hic/output)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
+
+## Introduction
+
+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.
 
 The directories listed below will be created in the results directory
 after the pipeline has finished. All paths are relative to the top-level
@@ -191,12 +195,16 @@ reported in the MultiQC output for future traceability.
 
 **Output files:**
 
-* `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
+* `multiqc/`
+  * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+  * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+  * `multiqc_plots/`: directory containing static images from the report in various formats.
+
+## Pipeline information
+
+[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
+
+**Output files:**
 
 * `pipeline_info/`
   * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`,

docs/usage.md

 # nf-core/hic: Usage
 
+## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/hic/usage](https://nf-co.re/hic/usage)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
+
+## Introduction
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:
@@ -74,9 +80,7 @@ fails after three times then the pipeline is stopped.
 Use this parameter to choose a configuration profile. Profiles can give
 configuration presets for different compute environments.
 
-Several generic profiles are bundled with the pipeline which instruct
-the pipeline to use software packaged using different methods
-(Docker, Singularity, Conda) - see below.
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Conda) - see below.
 
 > We highly recommend the use of Docker or Singularity containers for full
 pipeline reproducibility, however when this is not possible, Conda is also supported.
@@ -104,9 +108,11 @@ installed and available on the `PATH`. This is _not_ recommended.
 * `singularity`
   * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
   * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
+* `podman`
+  * A generic configuration profile to be used with [Podman](https://podman.io/)
+  * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
 * `conda`
-  * Please only use Conda as a last resort i.e. when it's not possible to run the
-  pipeline with Docker or Singularity.
+  * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity or Podman.
   * A generic configuration profile to be used with [Conda](https://conda.io/docs/)
   * Pulls most software from [Bioconda](https://bioconda.github.io/)
 * `test`
@@ -151,15 +157,7 @@ process {
 See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html)
 for more information.
 
-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 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 above). 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-co.re/join/slack) on the
@@ -215,7 +213,7 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--inpu
 For example:
 
 ```bash
---single_end --reads '*.fastq'
+--single_end --input '*.fastq'
 ```
 
 It is not possible to run a mixture of single-end and paired-end files in one run.

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-1.2.2
+name: nf-core-hic-1.3.0dev
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -255,24 +255,17 @@ summary['Min Insert Size']  = params.min_insert_size
 summary['Max Insert Size']  = params.max_insert_size
 summary['Min CIS dist']     = params.min_cis_dist
 summary['Maps resolution']  = params.bin_size
-summary['Max Memory']       = params.max_memory
-summary['Max CPUs']         = params.max_cpus
-summary['Max Time']         = params.max_time
+summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
+if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
 summary['Output dir']       = params.outdir
+summary['Launch dir']       = workflow.launchDir
 summary['Working dir']      = workflow.workDir
-summary['Container Engine'] = workflow.containerEngine
-if(workflow.containerEngine)
-   summary['Container']     = workflow.container
-summary['Current home']     = "$HOME"
-summary['Current user']     = "$USER"
-summary['Current path']     = "$PWD"
-summary['Working dir']      = workflow.workDir
-summary['Output dir']       = params.outdir
 summary['Script dir']       = workflow.projectDir
-summary['Config Profile']   = workflow.profile
-if(workflow.profile == 'awsbatch'){
+summary['User']             = workflow.userName
+if (workflow.profile.contains('awsbatch')) {
     summary['AWS Region']   = params.awsregion
     summary['AWS Queue']    = params.awsqueue
+    summary['AWS CLI']      = params.awscli
 }
 summary['Config Profile'] = workflow.profile
 if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description

nextflow.config

@@ -80,7 +80,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/hic:1.2.2'
+process.container = 'nfcore/hic:dev'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -108,6 +108,9 @@ profiles {
     singularity.enabled = true
     singularity.autoMounts = true
   }
+  podman {
+    podman.enabled = true
+  }
   test { includeConfig 'conf/test.config' }
 }
 
@@ -150,7 +153,7 @@ manifest {
   description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.2.2'
+  version = '1.3.0dev'
 }
 
 // Function to ensure that resource requirements don't go beyond

nextflow_schema.json

 {
-    "$schema": "https://json-schema.org/draft-07/schema",
+    "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/hic/master/nextflow_schema.json",
     "title": "nf-core/hic pipeline parameters",
     "description": "Analysis of Chromosome Conformation Capture data (Hi-C)",
@@ -295,7 +295,7 @@
                         "link",
                         "copy",
                         "copyNoFollow",
-                        "mov"
+                        "move"
                     ]
                 },
                 "name": {