From dcdf42cb4efc568c8c1d901b73ee440fc5434c7b Mon Sep 17 00:00:00 2001 From: Chris Wright Date: Fri, 29 Jan 2021 14:16:48 +0000 Subject: [PATCH] First sketch --- .dockerignore | 4 + .gitignore | 5 + .gitlab-ci.yml | 58 +++++++ Dockerfile | 15 ++ LICENSE | 373 ++++++++++++++++++++++++++++++++++++++++++ README.md | 34 ++++ nextflow.config | 19 +++ test_data/.gitkeep | 0 test_data/reads.fq.gz | Bin 0 -> 108 bytes workflow.nf | 84 ++++++++++ 10 files changed, 592 insertions(+) create mode 100644 .dockerignore create mode 100644 .gitignore create mode 100644 .gitlab-ci.yml create mode 100644 Dockerfile create mode 100644 LICENSE create mode 100644 README.md create mode 100644 nextflow.config create mode 100644 test_data/.gitkeep create mode 100644 test_data/reads.fq.gz create mode 100644 workflow.nf diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..345519b --- /dev/null +++ b/.dockerignore @@ -0,0 +1,4 @@ +.git +pipeline-nanopore-ref-isoforms +README.md +test_data diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e5d8ce0 --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +nextflow +.nextflow* +template-workflow +.*.swp +.*.swo diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000..c7739ea --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,58 @@ + +stages: + - build_and_run + - release + +image: ${IMAGE} +variables: + BASEIMAGE: ${CI_REGISTRY}/${CURRENT_TEMPLATE_IMAGE} + +build-image: + stage: build_and_run + variables: + before_script: + - apk add wget openjdk11 bash + - wget -qO- https://get.nextflow.io | bash + script: + - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY} + - TAG="${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}" + - docker build --no-cache -t "${TAG}" -f Dockerfile . --build-arg BASEIMAGE=${BASEIMAGE} + # run letting nextflow orchestrate the containers + - docker tag "${TAG}" "${CI_PROJECT_NAME}:latest" + - OUTPUT="template-workflow" + - ./nextflow run workflow.nf + -w ${OUTPUT}/workspace + -profile standard + --reads test_data/reads.fq.gz + --out_dir ${OUTPUT} + # push + - if [[ ${CI_COMMIT_BRANCH} == 'dev' ]]; then + SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}; + echo "Pushing ${SHATAG}"; + docker tag ${TAG} ${SHATAG}; + docker push ${SHATAG}; + fi; + only: + - branches + artifacts: + paths: + # Add the output directory for the test + - "template-workflow" + expire_in: 1 day + + +# Retag the image for git tags (releases) +release: + stage: release + script: + - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY} + - SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA} + - RELTAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_NAME} + - echo "Pulling ${SHATAG}" + - docker pull ${SHATAG} + - echo "Pushing ${TAG}" + - docker tag ${SHATAG} ${RELTAG} + - docker push ${RELTAG} + only: + - tags + diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..fedf94c --- /dev/null +++ b/Dockerfile @@ -0,0 +1,15 @@ +ARG BASEIMAGE=epi2melabs/base-workflow-image:latest +FROM $BASEIMAGE + +# Minimal install for example purposes +RUN \ + . $CONDA_DIR/etc/profile.d/mamba.sh \ + && micromamba activate \ + && micromamba install -y \ + pysam \ + -c anaconda -c conda-forge -c bioconda -q -y \ + && fix-permissions $CONDA_DIR \ + && fix-permissions $HOME + +USER $WF_UID +WORKDIR $HOME diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..a612ad9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,373 @@ +Mozilla Public License Version 2.0 +================================== + +1. Definitions +-------------- + +1.1. "Contributor" + means each individual or legal entity that creates, contributes to + the creation of, or owns Covered Software. + +1.2. "Contributor Version" + means the combination of the Contributions of others (if any) used + by a Contributor and that particular Contributor's Contribution. + +1.3. "Contribution" + means Covered Software of a particular Contributor. + +1.4. "Covered Software" + means Source Code Form to which the initial Contributor has attached + the notice in Exhibit A, the Executable Form of such Source Code + Form, and Modifications of such Source Code Form, in each case + including portions thereof. + +1.5. "Incompatible With Secondary Licenses" + means + + (a) that the initial Contributor has attached the notice described + in Exhibit B to the Covered Software; or + + (b) that the Covered Software was made available under the terms of + version 1.1 or earlier of the License, but not also under the + terms of a Secondary License. + +1.6. "Executable Form" + means any form of the work other than Source Code Form. + +1.7. "Larger Work" + means a work that combines Covered Software with other material, in + a separate file or files, that is not Covered Software. + +1.8. "License" + means this document. + +1.9. "Licensable" + means having the right to grant, to the maximum extent possible, + whether at the time of the initial grant or subsequently, any and + all of the rights conveyed by this License. + +1.10. "Modifications" + means any of the following: + + (a) any file in Source Code Form that results from an addition to, + deletion from, or modification of the contents of Covered + Software; or + + (b) any new file in Source Code Form that contains any Covered + Software. + +1.11. "Patent Claims" of a Contributor + means any patent claim(s), including without limitation, method, + process, and apparatus claims, in any patent Licensable by such + Contributor that would be infringed, but for the grant of the + License, by the making, using, selling, offering for sale, having + made, import, or transfer of either its Contributions or its + Contributor Version. + +1.12. "Secondary License" + means either the GNU General Public License, Version 2.0, the GNU + Lesser General Public License, Version 2.1, the GNU Affero General + Public License, Version 3.0, or any later versions of those + licenses. + +1.13. "Source Code Form" + means the form of the work preferred for making modifications. + +1.14. "You" (or "Your") + means an individual or a legal entity exercising rights under this + License. For legal entities, "You" includes any entity that + controls, is controlled by, or is under common control with You. For + purposes of this definition, "control" means (a) the power, direct + or indirect, to cause the direction or management of such entity, + whether by contract or otherwise, or (b) ownership of more than + fifty percent (50%) of the outstanding shares or beneficial + ownership of such entity. + +2. License Grants and Conditions +-------------------------------- + +2.1. Grants + +Each Contributor hereby grants You a world-wide, royalty-free, +non-exclusive license: + +(a) under intellectual property rights (other than patent or trademark) + Licensable by such Contributor to use, reproduce, make available, + modify, display, perform, distribute, and otherwise exploit its + Contributions, either on an unmodified basis, with Modifications, or + as part of a Larger Work; and + +(b) under Patent Claims of such Contributor to make, use, sell, offer + for sale, have made, import, and otherwise transfer either its + Contributions or its Contributor Version. + +2.2. Effective Date + +The licenses granted in Section 2.1 with respect to any Contribution +become effective for each Contribution on the date the Contributor first +distributes such Contribution. + +2.3. Limitations on Grant Scope + +The licenses granted in this Section 2 are the only rights granted under +this License. No additional rights or licenses will be implied from the +distribution or licensing of Covered Software under this License. +Notwithstanding Section 2.1(b) above, no patent license is granted by a +Contributor: + +(a) for any code that a Contributor has removed from Covered Software; + or + +(b) for infringements caused by: (i) Your and any other third party's + modifications of Covered Software, or (ii) the combination of its + Contributions with other software (except as part of its Contributor + Version); or + +(c) under Patent Claims infringed by Covered Software in the absence of + its Contributions. + +This License does not grant any rights in the trademarks, service marks, +or logos of any Contributor (except as may be necessary to comply with +the notice requirements in Section 3.4). + +2.4. Subsequent Licenses + +No Contributor makes additional grants as a result of Your choice to +distribute the Covered Software under a subsequent version of this +License (see Section 10.2) or under the terms of a Secondary License (if +permitted under the terms of Section 3.3). + +2.5. Representation + +Each Contributor represents that the Contributor believes its +Contributions are its original creation(s) or it has sufficient rights +to grant the rights to its Contributions conveyed by this License. + +2.6. Fair Use + +This License is not intended to limit any rights You have under +applicable copyright doctrines of fair use, fair dealing, or other +equivalents. + +2.7. Conditions + +Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted +in Section 2.1. + +3. Responsibilities +------------------- + +3.1. Distribution of Source Form + +All distribution of Covered Software in Source Code Form, including any +Modifications that You create or to which You contribute, must be under +the terms of this License. You must inform recipients that the Source +Code Form of the Covered Software is governed by the terms of this +License, and how they can obtain a copy of this License. You may not +attempt to alter or restrict the recipients' rights in the Source Code +Form. + +3.2. Distribution of Executable Form + +If You distribute Covered Software in Executable Form then: + +(a) such Covered Software must also be made available in Source Code + Form, as described in Section 3.1, and You must inform recipients of + the Executable Form how they can obtain a copy of such Source Code + Form by reasonable means in a timely manner, at a charge no more + than the cost of distribution to the recipient; and + +(b) You may distribute such Executable Form under the terms of this + License, or sublicense it under different terms, provided that the + license for the Executable Form does not attempt to limit or alter + the recipients' rights in the Source Code Form under this License. + +3.3. Distribution of a Larger Work + +You may create and distribute a Larger Work under terms of Your choice, +provided that You also comply with the requirements of this License for +the Covered Software. If the Larger Work is a combination of Covered +Software with a work governed by one or more Secondary Licenses, and the +Covered Software is not Incompatible With Secondary Licenses, this +License permits You to additionally distribute such Covered Software +under the terms of such Secondary License(s), so that the recipient of +the Larger Work may, at their option, further distribute the Covered +Software under the terms of either this License or such Secondary +License(s). + +3.4. Notices + +You may not remove or alter the substance of any license notices +(including copyright notices, patent notices, disclaimers of warranty, +or limitations of liability) contained within the Source Code Form of +the Covered Software, except that You may alter any license notices to +the extent required to remedy known factual inaccuracies. + +3.5. Application of Additional Terms + +You may choose to offer, and to charge a fee for, warranty, support, +indemnity or liability obligations to one or more recipients of Covered +Software. However, You may do so only on Your own behalf, and not on +behalf of any Contributor. You must make it absolutely clear that any +such warranty, support, indemnity, or liability obligation is offered by +You alone, and You hereby agree to indemnify every Contributor for any +liability incurred by such Contributor as a result of warranty, support, +indemnity or liability terms You offer. You may include additional +disclaimers of warranty and limitations of liability specific to any +jurisdiction. + +4. Inability to Comply Due to Statute or Regulation +--------------------------------------------------- + +If it is impossible for You to comply with any of the terms of this +License with respect to some or all of the Covered Software due to +statute, judicial order, or regulation then You must: (a) comply with +the terms of this License to the maximum extent possible; and (b) +describe the limitations and the code they affect. Such description must +be placed in a text file included with all distributions of the Covered +Software under this License. Except to the extent prohibited by statute +or regulation, such description must be sufficiently detailed for a +recipient of ordinary skill to be able to understand it. + +5. Termination +-------------- + +5.1. The rights granted under this License will terminate automatically +if You fail to comply with any of its terms. However, if You become +compliant, then the rights granted under this License from a particular +Contributor are reinstated (a) provisionally, unless and until such +Contributor explicitly and finally terminates Your grants, and (b) on an +ongoing basis, if such Contributor fails to notify You of the +non-compliance by some reasonable means prior to 60 days after You have +come back into compliance. Moreover, Your grants from a particular +Contributor are reinstated on an ongoing basis if such Contributor +notifies You of the non-compliance by some reasonable means, this is the +first time You have received notice of non-compliance with this License +from such Contributor, and You become compliant prior to 30 days after +Your receipt of the notice. + +5.2. If You initiate litigation against any entity by asserting a patent +infringement claim (excluding declaratory judgment actions, +counter-claims, and cross-claims) alleging that a Contributor Version +directly or indirectly infringes any patent, then the rights granted to +You by any and all Contributors for the Covered Software under Section +2.1 of this License shall terminate. + +5.3. In the event of termination under Sections 5.1 or 5.2 above, all +end user license agreements (excluding distributors and resellers) which +have been validly granted by You or Your distributors under this License +prior to termination shall survive termination. + +************************************************************************ +* * +* 6. Disclaimer of Warranty * +* ------------------------- * +* * +* Covered Software is provided under this License on an "as is" * +* basis, without warranty of any kind, either expressed, implied, or * +* statutory, including, without limitation, warranties that the * +* Covered Software is free of defects, merchantable, fit for a * +* particular purpose or non-infringing. The entire risk as to the * +* quality and performance of the Covered Software is with You. * +* Should any Covered Software prove defective in any respect, You * +* (not any Contributor) assume the cost of any necessary servicing, * +* repair, or correction. This disclaimer of warranty constitutes an * +* essential part of this License. No use of any Covered Software is * +* authorized under this License except under this disclaimer. * +* * +************************************************************************ + +************************************************************************ +* * +* 7. Limitation of Liability * +* -------------------------- * +* * +* Under no circumstances and under no legal theory, whether tort * +* (including negligence), contract, or otherwise, shall any * +* Contributor, or anyone who distributes Covered Software as * +* permitted above, be liable to You for any direct, indirect, * +* special, incidental, or consequential damages of any character * +* including, without limitation, damages for lost profits, loss of * +* goodwill, work stoppage, computer failure or malfunction, or any * +* and all other commercial damages or losses, even if such party * +* shall have been informed of the possibility of such damages. This * +* limitation of liability shall not apply to liability for death or * +* personal injury resulting from such party's negligence to the * +* extent applicable law prohibits such limitation. Some * +* jurisdictions do not allow the exclusion or limitation of * +* incidental or consequential damages, so this exclusion and * +* limitation may not apply to You. * +* * +************************************************************************ + +8. Litigation +------------- + +Any litigation relating to this License may be brought only in the +courts of a jurisdiction where the defendant maintains its principal +place of business and such litigation shall be governed by laws of that +jurisdiction, without reference to its conflict-of-law provisions. +Nothing in this Section shall prevent a party's ability to bring +cross-claims or counter-claims. + +9. Miscellaneous +---------------- + +This License represents the complete agreement concerning the subject +matter hereof. If any provision of this License is held to be +unenforceable, such provision shall be reformed only to the extent +necessary to make it enforceable. Any law or regulation which provides +that the language of a contract shall be construed against the drafter +shall not be used to construe this License against a Contributor. + +10. Versions of the License +--------------------------- + +10.1. New Versions + +Mozilla Foundation is the license steward. Except as provided in Section +10.3, no one other than the license steward has the right to modify or +publish new versions of this License. Each version will be given a +distinguishing version number. + +10.2. Effect of New Versions + +You may distribute the Covered Software under the terms of the version +of the License under which You originally received the Covered Software, +or under the terms of any subsequent version published by the license +steward. + +10.3. Modified Versions + +If you create software not governed by this License, and you want to +create a new license for such software, you may create and use a +modified version of this License if you rename the license and remove +any references to the name of the license steward (except to note that +such modified license differs from this License). + +10.4. Distributing Source Code Form that is Incompatible With Secondary +Licenses + +If You choose to distribute Source Code Form that is Incompatible With +Secondary Licenses under the terms of this version of the License, the +notice described in Exhibit B of this License must be attached. + +Exhibit A - Source Code Form License Notice +------------------------------------------- + + This Source Code Form is subject to the terms of the Mozilla Public + License, v. 2.0. If a copy of the MPL was not distributed with this + file, You can obtain one at http://mozilla.org/MPL/2.0/. + +If it is not possible or desirable to put the notice in a particular +file, then You may include the notice in a location (such as a LICENSE +file in a relevant directory) where a recipient would be likely to look +for such a notice. + +You may add additional accurate notices of copyright ownership. + +Exhibit B - "Incompatible With Secondary Licenses" Notice +--------------------------------------------------------- + + This Source Code Form is "Incompatible With Secondary Licenses", as + defined by the Mozilla Public License, v. 2.0. diff --git a/README.md b/README.md new file mode 100644 index 0000000..5952956 --- /dev/null +++ b/README.md @@ -0,0 +1,34 @@ +# Workflow template + +This repository contains a nextflow workflow template and associated +container build. + +## Quickstart + +```bash +# build the container +CONTAINER_TAG=template-workflow +docker build \ + -t ${CONTAINER_TAG} -f Dockerfile \ + --build-arg BASEIMAGE=epi2melabs/base-workflow-image:latest \ + . +``` + +The `BASEIMAGE` argument here can be changed to use an alternative image. + + +The template includes a simple workflow that outputs a file with the lengths +of sequences contained in a .fastq.gz file. +``` +# run the pipeline with the test data +OUTPUT=template-workflow +nextflow run workflow.nf \ + -w ${OUTPUT}/workspace \ + -profile standard \ + --reads test_data/reads.fq.gz \ + --out_dir ${OUTPUT} +``` + +The output of the pipeline will be found in `./template-workflow` for the above +example. This directory contains the nextflow working directories alongside +the two primary outputs of the pipeline. diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 0000000..5c4649d --- /dev/null +++ b/nextflow.config @@ -0,0 +1,19 @@ + +process { + withLabel:containerCPU { + container = 'workflow-template:latest' + } +} + +profiles { + // the "standard" profile is used implicitely by nextflow + // if no other profile is given on the CLI + standard { + docker { + enabled = true + // this ensures container is run as host user and group, but + // also adds host user to the within-container group + runOptions = "--user \$(id -u):\$(id -g) --group-add 100" + } + } +} diff --git a/test_data/.gitkeep b/test_data/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/test_data/reads.fq.gz b/test_data/reads.fq.gz new file mode 100644 index 0000000000000000000000000000000000000000..f4dc3d55e7616d474fddecfbaf9792cc7439ea9d GIT binary patch literal 108 zcmb2|=3rp}f&Xj_PR>jW{tU$$UcNqtPl}#gdKUDgh@r4&hm5m>jmC9}6Q%5*7c!|S rFuHeegq#r3VF_gwHfiQ)JK!R^lVMWZtxq{XW8~4ylV)HB8xJA?$s!yM literal 0 HcmV?d00001 diff --git a/workflow.nf b/workflow.nf new file mode 100644 index 0000000..f8b87e5 --- /dev/null +++ b/workflow.nf @@ -0,0 +1,84 @@ +#!/usr/bin/env extflow + +// Developer notes +// +// This template workflow provides a basic structure to copy in order +// to create a new workflow. Current recommended pratices are: +// i) create a simple command-line interface. +// ii) include an abstract workflow scope named "pipeline" to be used +// in a module fashion. +// iii) a second concreate, but anonymous, workflow scope to be used +// as an entry point when using this workflow in isolation. + +nextflow.enable.dsl = 2 + +params.help = "" + +if(params.help) { + log.info '' + log.info 'Workflow template' + log.info '' + log.info 'Usage: ' + log.info ' nextflow run workflow.nf [options]' + log.info '' + log.info 'Script Options: ' + log.info ' --fastq FILE Path to FASTQ file' + log.info ' --out_dir DIR Path for output' + log.info '' + + return +} + + +process readSeqs { + // Just write a file with sequence lengths + label "containerCPU" + input: + file reads + output: + file "seqs.txt" + + """ + #!/usr/bin/env python + import pysam + with open("seqs.txt", 'w') as fh: + for rec in pysam.FastxFile("$reads"): + fh.write("{}\\t{}\\n".format(rec.name, len(rec.sequence))) + """ +} + + + +// See https://github.com/nextflow-io/nextflow/issues/1636 +// This is the only way to publish files from a workflow whilst +// decoupling the publish from the process steps. +process output { + // publish inputs to output directory + + publishDir "${params.out_dir}", mode: 'copy', pattern: "*" + input: + file fname + output: + file fname + """ + echo "Writing output files" + """ +} + + +// workflow module +workflow pipeline { + take: + reads + main: + seqs = readSeqs(reads) + emit: + seqs +} + +// entrypoint workflow +workflow { + reads = channel.fromPath(params.reads, checkIfExists:true) + results = pipeline(reads) + output(results) +}