add illumina docker test #44
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fmalmeida
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May 18, 2023
* add illumina docker test (#44) * Update github actions for testing profiles (#46) * add illumina docker test * add other workflows as template * update sreads singularity test action * update lreads test actions * add hybrid test actions * remove unnecessary comments * 30 change to unicycler v050 (#45) * update version information * remove old spades binary for new unicycler version * update dockerfile to use new conda recipe * add testing profiles * working conda installation * update multiqc report * fixed docker image * increase asked cpus * Update nextflow_schema.json * decrease expected genome size * fix long reads assemblers installation * split long reads samplesheets * flye require 10.GB RAM * update workflows * easimon do not work in macos * update java * small update for tests * canu needs 4 cpus * update genome size value * split samplesheet in ont & pacbio * split proflies in ont & pacbio (hybrid) * delete unused files * new docker image has new python version * docker image fixed * skip flye tht requires much memory * fixed pacbio execution * revert to ubuntu * canu also is too much for git actions * remove unnecessary files * modify pilon polish script to run on number of desired rounds * fix output namings * fix outputs * pacbio profile working * update pilon info in docs * update changelog * upload yml with version of installed tools * update docs * use quast to save resulting assemblies
fmalmeida
added a commit
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Dec 24, 2023
* 31 new directory called final output (#48) * add illumina docker test (#44) * Update github actions for testing profiles (#46) * add illumina docker test * add other workflows as template * update sreads singularity test action * update lreads test actions * add hybrid test actions * remove unnecessary comments * 30 change to unicycler v050 (#45) * update version information * remove old spades binary for new unicycler version * update dockerfile to use new conda recipe * add testing profiles * working conda installation * update multiqc report * fixed docker image * increase asked cpus * Update nextflow_schema.json * decrease expected genome size * fix long reads assemblers installation * split long reads samplesheets * flye require 10.GB RAM * update workflows * easimon do not work in macos * update java * small update for tests * canu needs 4 cpus * update genome size value * split samplesheet in ont & pacbio * split proflies in ont & pacbio (hybrid) * delete unused files * new docker image has new python version * docker image fixed * skip flye tht requires much memory * fixed pacbio execution * revert to ubuntu * canu also is too much for git actions * remove unnecessary files * modify pilon polish script to run on number of desired rounds * fix output namings * fix outputs * pacbio profile working * update pilon info in docs * update changelog * upload yml with version of installed tools * update docs * use quast to save resulting assemblies * include citation information (#51) * Update README.md * update config
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