nextflow

A DSL for data-driven computational pipelines

APACHE-2.0 License

Stars
2.5K
Committers
164
View Code on GitHub Visit Website
Ecosystems: Docker, Groovy, Amazon Web Services

Bot releases are hidden (Show)

nextflow - Version 0.18.0

Published by pditommaso over 8 years ago

  • Added legacy option to docker configuration properties.
    Added support for --cpuset-cpus Docker command line option. See #115
  • Added region option to AWS S3 config properties #116
  • Added support for AWS S3 multipart uploads #112
  • Added NXF_TRACE to enable application trace logging
  • Added experimental support for Shifter containers
  • Added experimental support for HTCondor scheduler
  • Fixed Input file names staged into a subdirectory are not expanded properly #111
  • Fixed Main script class name collides with variable names in global scope #113
  • Fixed config file having a name as a top level config options raise a MissingPropertyException #117
  • Fixed Process script errors should not be ignored #119
  • Fixed timeline margin for long labels - fix #120
  • Fixed Process start time is not reported correctly when using the Ignite executor #122
  • Fixed Allow for a per-job memory limit for LSF executor #123
  • Fixed Memory reservation should not be divided by the number of cpus #124
  • Fixed Mixed content errors if timeline.html served over HTTPS #127
  • Fixed Nextflow won't start if a proxy URL env variable contains a trailing slash #109
  • Set poolSize as the number of avail cpus
  • Set java.io.tmpdir to the same path as NXF_TEMP
  • Updated Apache Ignite to version 1.5.0
  • Updated Logback to version 1.1.6
  • Updated Slf4j to version 1.7.21
  • Updated JGit to version 4.3.0.201604071810-r
nextflow - Version 0.17.3

Published by pditommaso over 8 years ago

  • Fixed task status in the trace file when execution is retried #107
  • Improved Ignite scheduling and node resources allocation
  • Upgraded Logback to version 1.1.5
  • Upgrade Slf4j to version 1.7.16
nextflow - Version 0.17.2

Published by pditommaso over 8 years ago

  • Fixed Channel.subscribe is invoked after the Workflow.onComplete handler #105
  • Changed default trace file name to trace.txt #106
  • Changed launcher classpath cache file under user home
  • Added JobStealingFailoverSpi to Ignite executor
  • Update JGit to version 4.2.0
nextflow - Version 0.17.1

Published by pditommaso over 8 years ago

  • Fixed splitText performance issue #102
  • Fixed execution hang when a process script block report and error and retry error strategy is set
  • Added support for partition to SLURM executor #101
  • Use a dedicated reentrant lock to handle task completion event
nextflow - Version 0.17.0

Published by pditommaso almost 9 years ago

  • Fixed PBS/Torque executor does not parse correctly job IDs #96
  • Fixed issue when TraceFileObsever tries to access task context metadata on task completion #98
  • Fixed support for Git local bare repositories #95
  • Fixed single quotes in file names result in a script error #99
  • Added workflow.sessionId and workflow.resume attributes #94
  • Added output into multiple channels #97
  • Added attempt field to execution trace file
  • Do not allow output clause to reference files outside the process working directory (see #91)
nextflow - Version 0.16.5

Published by pditommaso almost 9 years ago

  • Fixed race condition when creating cached launcher classpath file
  • Fixed run for local repositories
  • Enhanced output file handling #91
  • Set thread pool size to avail cpus +1
  • Removed config object from remote session that was causing a serialization issue
  • Upgraded Slf4j to version 1.7.13
nextflow - Version 0.16.4

Published by pditommaso almost 9 years ago

  • Use batch strategy to kill pending cluster jobs on termination #93
  • Added support for Git Large File Storage (LFS) extension #82
  • Added configurable thread pool factory #92
nextflow - Version 0.16.3

Published by pditommaso almost 9 years ago

  • Fixed #90. System user.dir property is cached causing unexpected behaviour.
  • Allow directories in a process input file name declaration. See #91.
  • Improved build script for local snapshot deployment.
  • Updated cli-args test.
nextflow - Version 0.16.2

Published by pditommaso almost 9 years ago

  • Fixed #87. Include current configuration profile option in the workflow metadata.
  • Fixed #86. Failure if work dir contains one or more blank characters.
  • Fixed #76. Include process name and tag information in process wrapper script.
nextflow - Version 0.16.1

Published by pditommaso almost 9 years ago

  • Fixed issue #85. Directive publishDir can't access process local variables.
  • Fixed wrong error message when trying to run a project sticked on a specific revision.
  • Fixed IllegalArgumentException: other must be an instance of com.upplication.s3fs.S3Path exception when publishing to a S3 path.
  • Fixed indentation in repo info command.
nextflow - Version 0.16.0

Published by pditommaso almost 9 years ago

  • Added ability to resubmit task executions changing resource requirements. See #70.
  • Added support for private SCM servers and private Gitlab repositories. See #38.
  • Added workflow metadata and execution onComplete notification handler. See #79.
  • Added publishDir directive. See #81.
  • Added extension method mklink to create file system links.
  • Added Apache Ignite based executor.
  • Removed deprecated GridGain executor.
  • Updated Capsule to version 1.0.1.
nextflow - Version 0.16.0-RC1

Published by pditommaso almost 9 years ago

nextflow - Version 0.15.6

Published by pditommaso about 9 years ago

  • Fixed #78. Command line parsing of parameters does not handle some strings properly.
  • Fixed #80. Command line argument containing a glob pattern is expanded even when escaped or enclosed in quote characters.
nextflow - Version 0.15.5

Published by pditommaso about 9 years ago

  • Fixed #74. Operator "spread" hangs when it is applied to a singleton channel.
nextflow - Version 0.15.4

Published by pditommaso about 9 years ago

  • Fixed #72. Adding cache support for collectFile operator.
  • Added experimental operator until
  • Added self-update in the command usage help
  • Updated Capsule to version 1.0
  • Updated to Gradle 2.7
nextflow - Version 0.15.3

Published by pditommaso about 9 years ago

  • Merged #68. Add engineOptions setting to Docker configuration.
nextflow - Version 0.15.2

Published by pditommaso about 9 years ago

  • Improved groupTuple operator adding the support of size and remainder parameters.
  • Fixed issue #47. Creation of scratch folder on Mac OS-X.
  • Fixed issue #64. Channel.fromPath throws an exception when curly brackets glob pattern is used with a S3 path.
  • Fixed issue #65. An input file that is staged from a foreign file system lost it's original name.
  • Fixed issue #66. Git submodules are not cloned/updated when a pipeline project is pulled from a remote repository.
  • Fixed minor issue when evaluating config lazy property with no binding object.
  • Updated Capsule to latest version () fixing an issue that was preventing to add a custom path to the application classpath.
  • Added Path matches extension method [experimental].
  • Added support for into parameter to splitXxx operators.
  • Changed signature of close operator so that it returns the channel to which it is applied.
nextflow - Version 0.15.1

Published by pditommaso about 9 years ago

  • Added feature #60 - Implements support for Gitlab source code management platform.
  • Added support for disk directive to crg executor.
  • Fixed issue #57 - Creation folder lock must be a singleton instance.
  • Fixed issue #62 - Operator hangs for negative values or when it is greater or equals to the total number of emitted items.
  • Fixed an exception when output file is specified with variable identifier e.g. output: file(x) into channel
nextflow - Version 0.15.0

Published by pditommaso about 9 years ago

  • Issue #56 - Added method all() to params object
  • Issue #57 - Processes having identical commands and inputs are given the same hash key
  • Issue #59 - Enhanced output val declaration adding support for value literals and value expressions
  • Fixed minor issue when deleting pipeline repo with drop command
  • Removed deprecated share process clause
  • Updated JGit to version 4.0.1
nextflow - Version 0.14.4

Published by pditommaso over 9 years ago

  • Fixed issue #54 - Nextflow installer does not work when running behind a proxy server
  • Upgraded Capsule package manager to version 1.0-rc2
Package Rankings
Top 6.54% on Repo1.maven.org
Top 4.6% on Proxy.golang.org
Badges
Extracted from project README
Nextflow CI Nextflow version Nextflow Twitter Nextflow Publication install with bioconda Nextflow license
Related Projects
devops-resources

DevOps resources - Linux, Jenkins, AWS, SRE, Prometheus, Docker, Python, Ansible, Git, Kubernetes...

07 Jan 2019 8,538