Quandenser-pipeline v0.0837

Quandenser-pipeline v0.0837

Bugfixes:

• Updated cluster cpu/time parameter names in GUI

Changes:

• Added support for parallel MaRaCluster jobs for precursor m/z bins

NOTE: Further testing is still required for stability, due to unknown effects from previous changes with Quandenser, such as resume and docker implementation

Quandenser-pipeline v0.0836

Quandenser-pipeline v0.0836

More testing has been done and more bugs found.

Bugfixes

• Fixed bad indexing in NF pipeline from previous changes (broke several things). You can now run mixed mzML + raw files without any hiccups.
• Some "WARNING: could not open input file" fixes for Quandenser
• Some fixes for Mac OS in GUI
• Stability improvements in both GUI and pipeline
• Better syncing in pipeline, should not affect Quandenser with unsynced files

Changes:

• Added parallelization on boxcar and set MaxForks for it.
• Added images to WIKI

NOTE: Further testing is still required for stability, due to unknown effects from previous changes with Quandenser, such as resume and docker implementation

Quandenser-pipeline v0.0835

Quandenser-pipeline v0.0835

Bugfixes

• Fixed wrong directory binds in shell script, resulting in crashes and wrong mountings.
• Fixed WSL2 compatibility (#31)
• Fixed pull backwards-compatibility with singhub (#32). Needs further testing
• Fixed wrong order of execution in nextflow pipeline (making dirs)
• Fixed GUI after renaming of parameters
• Fixed CONFIG_LOCATION path in shell script when running the pipeline in GUI
• Added checks for dependencies (jq for automatic updating and java, for running nextflow)
• Fixed so there will not be double install of GO when installing singularity again / updating it.

** Quickfix java version check for older versions.

NOTE: Further testing is still required for stability, which will require more time due to computational limitations at the moment

Quandenser-pipeline v0.0834

Quandenser-pipeline v0.0834

Credit to Lukas Käll

• Added offline installation and installing the image "gui-free", to use it as a CLI.
• Updated Quandenser_pipeline.sh file for users to choose what to install. This chang should be downloaded automatically if you run your any previous versions of the shell script and up to v0.08 beta.

Credit to Matthew The

• Added docker support for the image and improved CLI.
• Fixed Dinosaur permission
• Fixed GUI problems with the dark style layout
• Improved nextflow pipeline and parallel processing

Quandenser-pipeline v0.0833

Quandenser-pipeline v0.0833

Changes in building the image

• Building quandenser during build
• Updated quandenser

Quandenser-pipeline v0.0832

Quandenser-pipeline v0.0832

Changes in the GUI and shell

• Fixed so the config files are imported from user-specified folder by setting the config_path in the shell file

Changes in building the image

• Fixed depreciated python + modules during building of the image

Quandenser-pipeline v0.0831

Quandenser-pipeline v0.0831

Changes in the GUI

• Fixed a bug in the qstyledark theme where the QComboBoxes were way too large

• Added experimental workload managers from here https://www.nextflow.io/docs/latest/executor.html

Quandenser-pipeline v0.083

Changes in the shell script:

Minor changes:

• Changed singularity install version from 3.2.1 to 3.4.1, which is latest stable for the pipeline tested.

• Added mount points in all singularity calls

Changes in the image:

Minor changes:

• Changed hardcoded /tmp directory to the environment variable "WINE_TMPDIR". By setting the variable, both the image and all calls from nextflow imports the variable to use within the image. The imports can be found here in the configuration file.

• Fixed some bugs with environmental variables not being imported

Quandenser-pipeline v0.0821 HOTFIX

Changes in the image:

Minor changes:

• HOTFIX: encoding problem in command_wrapper.py causes crash in quandenser_parallel_3 during naming convention of files. Commit ed134f5 SHOULD fix this issue.

Quandenser-pipeline v0.082

Changes in building the image:

Minor changes:

• command_wrapper.py added to the image. The purpose is to fix some common errors found in the pipeline.

Changes in the shell script:

Minor changes:

• Added messages when the user enables some options

• The installed singularity version by the shell script is now fixed on singularity version v3.2.1, since the latest version v3.4.0 has some restrictions on what you can interact with on the host computer. This includes the "running jobs" tab and the button which can kill the processes. This means you would have to kill all processes manually, if you have v3.4.0 installed

Changes in the image:

Major changes:

• Major improvements with parallel processing. See enhancement #19. A positive side effect of this change is that the parallel processing is way more efficient with memory, so that means you can run larger data sets with the parallel option!

Minor changes:

• This is a "minor" change, but this change fixes 2 very important and "pipeline breaking" bugs, namely issue #3 and issue #23. MSconvert, quandenser_parallel_1 and quandenser_parallel_3 will now be executed through a "wrapper" script, which checks for known errors which causes the issue. The script is found here. This should also prevent zombie processes from happening.

• You can now choose in tab 3 if you want to publish the files (aka copy them to the output directory from work directory). This is an useful option to have if you have limited storage space on the computer you are working on and don't want some of the "intermediate" files. Note that you still have to remove the work directory manually when you are done.

• The pipeline now allows one crash on msconvert, quandenser_parallel_1 and quandenser_parallel_3, due to the known errors and command_wrapper. This also solves in most cases issue #22, where singularity fails to mount the image when running many parallel processes. It is sometimes rare, but if the pipeline fails to mount the image twice in a row on the same process, the pipeline will crash. This fix helps at least computers which has that issue from crashing 100% of the time, to a lot less than that.