nf-EAGER v${version}

nf-core/EAGER2 v${version}

Run Name: $runName

<% if (!success){ out << """

nf-EAGER execution completed unsuccessfully!

nf-core/EAGER2 execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

The full error message was:

${errorReport}

diff --git a/assets/email_template.txt b/assets/email_template.txt index 106c804cc..d237ca6a0 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,13 +1,13 @@ ======================================== - nf-EAGER v${version} + nf-core/EAGER2 v${version} ======================================== Run Name: $runName <% if (success){ - out << "## nf-EAGER execution completed successfully! ##" + out << "## nf-core/EAGER2 execution completed successfully! ##" } else { out << """#################################################### -## nf-EAGER execution completed unsuccessfully! ## +## nf-core/EAGER2 execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: $exitStatus. The full error message was: @@ -19,7 +19,7 @@ ${errorReport} <% if (!success){ out << """#################################################### -## nf-EAGER execution completed unsuccessfully! ## +## nf-core/EAGER2 execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: $exitStatus. The full error message was: @@ -27,7 +27,7 @@ The full error message was: ${errorReport} """ } else { - out << "## nf-EAGER execution completed successfully! ##" + out << "## nf-core/EAGER2 execution completed successfully! ##" } %> @@ -52,5 +52,5 @@ Software Versions: <% out << software_versions.collect{ k,v -> " - $k: $v" }.join("\n") %> -- -nf-EAGER -https://github.com/apeltzer/nf-EAGER +nf-core/EAGER2 +https://github.com/nf-core/EAGER2 diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 6bf34fb13..73085dbc3 100755 --- a/bin/scrape_software_versions.py +++ b/bin/scrape_software_versions.py @@ -4,13 +4,13 @@ import re regexes = { - 'nf-EAGER': ['v_pipeline.txt', r"(\S+)"], + 'nf-core/EAGER2': ['v_pipeline.txt', r"(\S+)"], 'Nextflow': ['v_nextflow.txt', r"(\S+)"], 'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"], 'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"], } results = OrderedDict() -results['nf-EAGER'] = 'N/A' +results['nf-core/EAGER2'] = 'N/A' results['Nextflow'] = 'N/A' results['FastQC'] = 'N/A' results['MultiQC'] = 'N/A' @@ -26,8 +26,8 @@ # Dump to YAML print (''' id: 'nf-eager-software-versions' -section_name: 'nf-EAGER Software Versions' -section_href: 'https://github.com/apeltzer/nf-EAGER' +section_name: 'nf-core/EAGER2 Software Versions' +section_href: 'https://github.com/nf-core/EAGER2' plot_type: 'html' description: 'are collected at run time from the software output.' data: | diff --git a/conf/base.config b/conf/base.config index 001a42288..3b75acb83 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,6 +1,6 @@ /* * ------------------------------------------------- - * nf-EAGER Nextflow base config file + * nf-core/EAGER2 Nextflow base config file * ------------------------------------------------- * A 'blank slate' config file, appropriate for general * use on most high performace compute environments. diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml index 81e48a962..fc0e652b4 100644 --- a/conf/multiqc_config.yaml +++ b/conf/multiqc_config.yaml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-EAGER + This report has been generated by the nf-core/EAGER2 analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: nf-eager-software-versions: order: -1000 diff --git a/docs/README.md b/docs/README.md index c82a84cc9..234013904 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,6 +1,6 @@ -# nf-EAGER Documentation +# nf-core/EAGER2 Documentation -The nf-EAGER documentation is split into the following files: +The nf-core/EAGER2 documentation is split into the following files: 1. [Installation](installation.md) 2. Pipeline configuration diff --git a/docs/configuration/adding_your_own.md b/docs/configuration/adding_your_own.md index e73c4e9ae..54b4e1371 100644 --- a/docs/configuration/adding_your_own.md +++ b/docs/configuration/adding_your_own.md @@ -1,4 +1,4 @@ -# nf-EAGER: Configuration for other clusters +# nf-core/EAGER2: Configuration for other clusters It is entirely possible to run this pipeline on other clusters, though you will need to set up your own config file so that the pipeline knows how to work with your cluster. @@ -35,7 +35,7 @@ process { To run the pipeline, several software packages are required. How you satisfy these requirements is essentially up to you and depends on your system. If possible, we _highly_ recommend using either Docker or Singularity. ### Docker -Docker is a great way to run nf-EAGER, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems. +Docker is a great way to run nf-core/EAGER2, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems. Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required. @@ -43,10 +43,10 @@ First, install docker on your system: [Docker Installation Instructions](https:/ Then, simply run the analysis pipeline: ```bash -nextflow run apeltzer/nf-EAGER -profile docker --reads '' +nextflow run nf-core/EAGER2 -profile docker --reads '' ``` -Nextflow will recognise `apeltzer/nf-EAGER` and download the pipeline from GitHub. The `-profile docker` configuration lists the [quay.io/nf-core/nf-eager](https://hub.docker.com/r/quay.io/nf-core/nf-eager/) image that we have created and is hosted at dockerhub, and this is downloaded. +Nextflow will recognise `nf-core/EAGER2` and download the pipeline from GitHub. The `-profile docker` configuration lists the [nfcore/eager2](https://hub.docker.com/r/nfcore/eager2/) image that we have created and is hosted at dockerhub, and this is downloaded. The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.3`. This uses pipeline code and docker image from this tagged version. @@ -63,12 +63,12 @@ process { The variable `wf_container` is defined dynamically and automatically specifies the image tag if Nextflow is running with `-r`. -A test suite for docker comes with the pipeline, and can be run by moving to the [`tests` directory](https://github.com/apeltzer/nf-EAGER/tree/master/tests) and running `./run_test.sh`. This will download a small yeast genome and some data, and attempt to run the pipeline through docker on that small dataset. This is automatically run using [Travis](https://travis-ci.org/apeltzer/nf-EAGER/) whenever changes are made to the pipeline. +A test suite for docker comes with the pipeline, and can be run by moving to the [`tests` directory](https://github.com/nf-core/EAGER2/tree/master/tests) and running `./run_test.sh`. This will download a small yeast genome and some data, and attempt to run the pipeline through docker on that small dataset. This is automatically run using [Travis](https://travis-ci.org/nf-core/EAGER2/) whenever changes are made to the pipeline. ### Singularity image Many HPC environments are not able to run Docker due to security issues. [Singularity](http://singularity.lbl.gov/) is a tool designed to run on such HPC systems which is very similar to Docker. Even better, it can use create images directly from dockerhub. -To use the singularity image for a single run, use `-with-singularity 'docker://apeltzer/nf-EAGER'`. This will download the docker container from dockerhub and create a singularity image for you dynamically. +To use the singularity image for a single run, use `-with-singularity 'docker://nfcore/eager2'`. This will download the docker container from dockerhub and create a singularity image for you dynamically. To specify singularity usage in your pipeline config file, add the following: @@ -88,13 +88,13 @@ If you intend to run the pipeline offline, nextflow will not be able to automati First, pull the image file where you have an internet connection: ```bash -singularity pull --name nf-eager.img docker://apeltzer/nf-EAGER +singularity pull --name eager2.img docker://nfcore/eager2 ``` Then transfer this file and run the pipeline with this path: ```bash -nextflow run /path/to/nf-eager -with-singularity /path/to/nf-eager.img +nextflow run /path/to/eager2 -with-singularity /path/to/eager2.img ``` @@ -120,8 +120,8 @@ conda config --add channels salilab #### 3) Create a conda environment, with all necessary packages: ```bash -conda create --name nf-eager_py2.7 python=2.7 -source activate nf-eager_py2.7 +conda create --name nf-core-eager2_py2.7 python=2.7 +source activate nf-core-eager2_py2.7 conda install --yes \ fastqc \ multiqc @@ -132,7 +132,7 @@ _(Feel free to adjust versions as required.)_ Once created, the conda environment can be activated before running the pipeline and deactivated afterwards: ```bash -source activate nf-eager_py2.7 +source activate nf-core-eager2_py2.7 # run pipeline source deactivate ``` diff --git a/docs/configuration/local.md b/docs/configuration/local.md index 073664a31..9ef9877f1 100644 --- a/docs/configuration/local.md +++ b/docs/configuration/local.md @@ -1,20 +1,20 @@ -# nf-EAGER: Local Configuration +# nf-core/EAGER2: Local Configuration If running the pipeline in a local environment, we highly recommend using either Docker or Singularity. ## Docker -Docker is a great way to run nf-EAGER, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems. +Docker is a great way to run nf-core/EAGER2, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems. -Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required. The nf-EAGER profile comes with a configuration profile for docker, making it very easy to use. This also comes with the required presets to use the AWS iGenomes resource, meaning that if using common reference genomes you just specify the reference ID and it will be autaomtically downloaded from AWS S3. +Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required. The nf-core/EAGER2 profile comes with a configuration profile for docker, making it very easy to use. This also comes with the required presets to use the AWS iGenomes resource, meaning that if using common reference genomes you just specify the reference ID and it will be automatically downloaded from AWS S3. First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/) Then, simply run the analysis pipeline: ```bash -nextflow run apeltzer/nf-EAGER -profile docker --reads '' +nextflow run nf-core/EAGER2 -profile docker --reads '' ``` -Nextflow will recognise `apeltzer/nf-EAGER` and download the pipeline from GitHub. The `-profile docker` configuration lists the [quay.io/nf-core/nf-eager](https://hub.docker.com/r/quay.io/nf-core/nf-eager/) image that we have created and is hosted at dockerhub, and this is downloaded. +Nextflow will recognise `nf-core/EAGER2` and download the pipeline from GitHub. The `-profile docker` configuration lists the [nf-core/eager2](https://hub.docker.com/r/nfcore/eager2/) image that we have created and is hosted at dockerhub, and this is downloaded. For more information about how to work with reference genomes, see [`docs/configuration/reference_genomes.md`](docs/configuration/reference_genomes.md). @@ -25,18 +25,18 @@ The public docker images are tagged with the same version numbers as the code, w ## Singularity image Many HPC environments are not able to run Docker due to security issues. [Singularity](http://singularity.lbl.gov/) is a tool designed to run on such HPC systems which is very similar to Docker. Even better, it can use create images directly from dockerhub. -To use the singularity image for a single run, use `-with-singularity 'docker://quay.io/nf-core/nf-eager'`. This will download the docker container from dockerhub and create a singularity image for you dynamically. +To use the singularity image for a single run, use `-with-singularity 'docker://nfcore/eager2'`. This will download the docker container from dockerhub and create a singularity image for you dynamically. If you intend to run the pipeline offline, nextflow will not be able to automatically download the singularity image for you. Instead, you'll have to do this yourself manually first, transfer the image file and then point to that. First, pull the image file where you have an internet connection: ```bash -singularity pull --name nf-eager.img docker://quay.io/nf-core/nf-eager +singularity pull --name nf-core-eager2.img docker://nfcore/eager2 ``` Then transfer this file and run the pipeline with this path: ```bash -nextflow run /path/to/nf-EAGER -with-singularity /path/to/nf-eager.img +nextflow run /path/to/nf-core/EAGER2 -with-singularity /path/to/nf-core-eager2.img ``` diff --git a/docs/configuration/reference_genomes.md b/docs/configuration/reference_genomes.md index 9ee77b495..95f230966 100644 --- a/docs/configuration/reference_genomes.md +++ b/docs/configuration/reference_genomes.md @@ -1,11 +1,11 @@ -# nf-EAGER: Reference Genomes Configuration +# nf-core/EAGER2: Reference Genomes Configuration -The nf-EAGER pipeline needs a reference genome for alignment and annotation. If not already available, start by downloading the relevant reference, for example from [illumina iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html). +The nf-core/EAGER2 pipeline needs a reference genome for alignment and annotation. If not already available, start by downloading the relevant reference, for example from [illumina iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html). The minimal requirements are a FASTA file. ## Adding paths to a config file -Specifying long paths every time you run the pipeline is a pain. To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline. +Specifying long paths every time you run the pipeline is a pain. To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline. Note that this genome key can also be specified in a config file if you always use the same genome. @@ -36,7 +36,7 @@ If possible, we recommend making this resource available on your cluster. We hav To add iGenomes to your config file, add the following line to the end of your config file: ```nextflow -includeConfig '/path/to/nf-EAGER/conf/igenomes.config' +includeConfig '/path/to/nf-core/EAGER2/conf/igenomes.config' ``` This works best when you have a `profile` set up in the pipeline - see [`nextflow.config`](../../nextflow.config). diff --git a/docs/installation.md b/docs/installation.md index c1e2864b7..5998b5707 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -1,6 +1,6 @@ -# nf-EAGER Installation +# nf-core/EAGER2 Installation -To start using the nf-EAGER pipeline, there are three steps described below: +To start using the nf-core/EAGER2 pipeline, there are three steps described below: 1. [Install Nextflow](#install-nextflow) 2. [Install the pipeline](#install-the-pipeline) @@ -26,10 +26,11 @@ mv nextflow ~/bin **You need NextFlow version >= 0.24 to run this pipeline.** -See [nextflow.io](https://www.nextflow.io/) and [NGI-NextflowDocs](https://github.com/SciLifeLab/NGI-NextflowDocs) for further instructions on how to install and configure Nextflow. +See [Nextflow documentation](https://www.nextflow.io/docs/latest/index.html) or the [nf-core website](https://nf-core.github.io/) for further instructions on how to install and configure Nextflow. +Join the gitter channels for some direct contact with developers: [nextflow channel](https://gitter.im/nextflow-io/nextflow) or [nf-core Lobby](https://gitter.im/nf-core/Lobby). ## 2) Install the Pipeline -This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if `apeltzer/nf-EAGER` is specified as the pipeline name. +This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if `nf-core/EAGER2` is specified as the pipeline name. ### Offline use diff --git a/docs/output.md b/docs/output.md index fb5977e22..d04702cf9 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,4 +1,4 @@ -# nf-EAGER +# nf-core/EAGER2 A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support. 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. diff --git a/docs/parameters.md b/docs/parameters.md index 8755b0222..f7ffbfbf8 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -1,4 +1,4 @@ -# Adjustable parameters for EAGER2 +# Adjustable parameters for nf-core/EAGER2 ## Read Clipping / Merging params.mergemethod = AdapterRemoval or ClipAndMerge (choice) diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md index bbac717e6..05ed79ad9 100644 --- a/docs/troubleshooting.md +++ b/docs/troubleshooting.md @@ -23,6 +23,6 @@ The pipeline can't take a list of multiple input files - it takes a glob express ## Extra resources and getting help If you still have an issue with running the pipeline then feel free to contact us. -Have look at the [pipeline website](https://github.com/apeltzer/nf-EAGER) to find out how. +Have look at the [pipeline website](https://github.com/nf-core/EAGER2) to find out how. If you have problems that are related to Nextflow and not our pipeline then check out the [Nextflow gitter channel](https://gitter.im/nextflow-io/nextflow) or the [google group](https://groups.google.com/forum/#!forum/nextflow). diff --git a/docs/usage.md b/docs/usage.md index 78f31065a..fc70dc994 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,4 +1,4 @@ -# nf-EAGER Usage +# nf-core/EAGER2 Usage ## General Nextflow info 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. @@ -12,7 +12,7 @@ NXF_OPTS='-Xms1g -Xmx4g' ## Running the pipeline The typical command for running the pipeline is as follows: ```bash -nextflow run apeltzer/nf-EAGER --reads '*_R{1,2}.fastq.gz' -profile docker +nextflow run nf-core/EAGER2 --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. diff --git a/environment.yml b/environment.yml index a8cd45576..74fee91d3 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: nf-core-eager +name: nf-core-eager2 channels: - defaults - conda-forge @@ -20,4 +20,4 @@ dependencies: - vcf2genome=0.91 - damageprofiler=0.3.11 - multiqc=1.5 - #Missing Schmutzi, Missing PMDTools, Missing SequenceTools \ No newline at end of file + #Missing Schmutzi, Missing PMDTools, Missing SequenceTools diff --git a/main.nf b/main.nf index cafd5c959..2bab6b3a9 100644 --- a/main.nf +++ b/main.nf @@ -1,14 +1,14 @@ #!/usr/bin/env nextflow /* ======================================================================================== - nf-EAGER + nf-core/EAGER2 ======================================================================================== EAGER2 Analysis Pipeline. Started 2018-06-05 #### Homepage / Documentation https://github.com/nf-core/EAGER2 #### Authors Alexander Peltzer apeltzer - https://github.com/apeltzer> - James Fellows-Yates - https://github.com/jfy133 + James A. Fellows Yates - https://github.com/jfy133 ---------------------------------------------------------------------------------------- */ @@ -93,7 +93,7 @@ Channel // Header log info log.info "=========================================" -log.info " nf-EAGER v${params.version}" +log.info " nf-core/EAGER2 v${params.version}" log.info "=========================================" def summary = [:] summary['Run Name'] = custom_runName ?: workflow.runName @@ -185,7 +185,7 @@ process fastqc { } /* - * STEP 2 - Adapter Clipping / Read Merging + * STEP 2 - Adapter Clipping / Read Merging */ if(params.mergemethod == 'AdapterRemoval'){ @@ -194,7 +194,7 @@ process adapter_removal { tag "$name" publishDir "${params.outdir}/02-Merging", mode: 'copy' - input: + input: set val(name), file(reads) from ch_read_files_clip output: @@ -209,14 +209,14 @@ process adapter_removal { #Combine files zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > ${prefix}.combined.fq.gz """ - + } else { //We use Clip&Merge then process clip_merge { tag "$name" publishDir "${params.outdir}/02-Merging", mode: 'copy' - input: + input: set val(name), file(reads) from ch_read_files_clip output: @@ -224,7 +224,7 @@ process clip_merge { script: """ - ClipAndMerge -in1 ${reads[0]} -in2 ${reads[1]} + ClipAndMerge -in1 ${reads[0]} -in2 ${reads[1]} -f ${params.clip.forward_adaptor} -r ${params.clip.reverse_adaptor} -trim3p ${params.clip.3pclip} -trim5p ${params.clip.5pclip} -l ${params.clip.readlength} -m ${params.clip.min_adap_overlap} -qt -q ${params.clip.min_read_quality} -log "ClipAndMergeStats.log" """ @@ -301,9 +301,9 @@ process output_documentation { workflow.onComplete { // Set up the e-mail variables - def subject = "[nf-EAGER] Successful: $workflow.runName" + def subject = "[nf-core/EAGER2] Successful: $workflow.runName" if(!workflow.success){ - subject = "[nf-EAGER] FAILED: $workflow.runName" + subject = "[nf-core/EAGER2] FAILED: $workflow.runName" } def email_fields = [:] email_fields['version'] = params.version @@ -352,11 +352,11 @@ workflow.onComplete { 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-EAGER] Sent summary e-mail to $params.email (sendmail)" + log.info "[nf-core/EAGER2] 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-EAGER] Sent summary e-mail to $params.email (mail)" + log.info "[nf-core/EAGER2] Sent summary e-mail to $params.email (mail)" } } @@ -370,6 +370,6 @@ workflow.onComplete { def output_tf = new File( output_d, "pipeline_report.txt" ) output_tf.withWriter { w -> w << email_txt } - log.info "[nf-EAGER] Pipeline Complete" + log.info "[nf-core/EAGER2] Pipeline Complete" } diff --git a/nextflow.config b/nextflow.config index 0db5aed47..b7fbb7205 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,7 +12,7 @@ params { version = '2.0' // Pipeline version nf_required_version = '0.29.0' // Minimum version of nextflow required - container = 'nfcore/eager2.0:latest' + container = 'nfcore/eager2:latest' //Pipeline options aligner = 'bwa' diff --git a/tests/run_test.sh b/tests/run_test.sh index 13379759d..eada3d365 100644 --- a/tests/run_test.sh +++ b/tests/run_test.sh @@ -84,7 +84,7 @@ else fi # Run name -run_name="Test nf-EAGER Run: "$(date +%s) +run_name="Test nf-core/EAGER2 Run: "$(date +%s) cmd="nextflow run $pipelinescript -resume -name \"$run_name\" $profile $dockerfl $singularityfl --reads \"${data_dir}/*.fastq.gz\"" echo "Starting nextflow... Command:"