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Created with Raphaël 2.2.030Oct164Sep28Aug27222120127330Jul2928221917161015May28Jul272516Aug76431Jul26Jun22211923Apr2221201716151328Mar272625242321201916152129Feb262418161512111028Jan26Sep171612316Aug141286131Jul3026252423221918171615121110983231May302928241716151465229Apr2623222120191817161520Mar1917161514131211109875Feb31Jan2522191815141312111098765427Dec26252417162Nov131Oct14Aug1311226Jul252429Jun2726258May16Mar1515Feb1413Jan121110529Nov212019181716151410Removed debugging code and fixed memory_per_thread assignmenttest_1.2.15test_1.2.15removed dev files -- files committed by mistakeupdated executor for all processestest_1.2.13 tes…test_1.2.13 test_1.2.14fixed memory assignment per thread to whole memory scaled to 0.7; updated queues for some processestest_1.2.12test_1.2.12all processes run on 128GB or higher machinestest_1.2.11test_1.2.11limit number of concurrent processes in trimreads, alignreads, and filterreads to 4 to help with memory issuesin convert_reads.py: assigned memory to working thread in damtool sort, similar to map_reads.pyquadruple memory used per thread in alignread step in mapreads.py scriptupdated main to use back python docker with entrypointUsing py36 docker with no-conda env and updating related files. Use nextflow 19Dummy commit -- to force updating masteradded beforeScript step to all processes which increase ulimit of open filescontainerizedcontainerizedupdated config to run ulimit -n 24000 which might help with the errors we get during trim reads.changed nextflow version to 22.x.yAdded argument to call of ifEmpty()Uncommented nextflow_version in astrocyte_pkg.ymlUse 256 queue only for trim reads step to avoid samtools call in map_reads.py:wqAdd missing port number to container image tags.Rewrite container image references in the workflow config files to use the official container registry.Merge branch 'containerized' into 'containerized'Added new Docker file for motif search (named meme-5.5.4) installed from source, with all the necessary changes to use the new container for motif search. Updated the command line arguments for meme-chip to use v5.x syntax.Merge branch 'containerized' of git.biohpc.swmed.edu:s219741/chipseq-analysis-containerized into containerizedFP push final changes to repo before moving.Update base image tag in Dockerfiles.Push in-development containerized workflowUpdate nextflow compatible version91-update-nf-to…91-update-nf-tower-tokenRevert nextflowUpdate nextflow versionUpdate nextflow versionUpdate nextflow versionFix tokenUpdate nextflow.configUpdate python testing versionsAdd in changes. Fix version Update workspaceIDUpdate nextflow versionUpdate nextflow.config with access tokenMerge branch 'dev' into 'master'publish_1.1.3publish_1.1.3get ready for release.noCidnoCid