Releases: emilyncosta/UNIFESP_NTM_newspecies-nf
Releases · emilyncosta/UNIFESP_NTM_newspecies-nf
v2.0.0-beta4
Full Changelog: v2.0.0-beta3...v2.0.0-beta4
v2.0.0-beta3
Full Changelog: v2.0.0-beta...v2.0.0-beta3
Update publication name
Update the pipeline to address reviewers comments [ci skip] (#10) * Reinitialize pipeline with nf-core template [ci skip] * install relevant modules [ci skip] * add the fully concatenated file [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * download assemblies using ncbi-datasets-cli [ci skip] * add more references for reviewer-assemblies [ci skip] * add download script [ci skip] * dev iteration [ci skip] * use baseline java8 for orthoani [ci skip] * add orthoani util modules [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * update the hardware req for trimmomatic [ci skip] * add ggdc results [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * restore spades in favor of util process for filtering [ci skip] * add post-spades utils [ci skip] * add post-spades utils [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * make fastgrep executable [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * test with latest checkm process [ci skip] * retry with 1.1.8 checkm and reduced tree [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * regenrate the ggdc results [ci skip] * add params and orthoani subworkflow [ci skip] * use a custom container [ci skip] * use lower resources [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add orthofinder [ci skip] * add orthofinder [ci skip] * add orthofinder [ci skip] * add orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthoani [ci skip]
Update pipeline to regenerate the results as per reviewers comments
Update the pipeline to address reviewers comments [ci skip] (#10) * Reinitialize pipeline with nf-core template [ci skip] * install relevant modules [ci skip] * add the fully concatenated file [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * download assemblies using ncbi-datasets-cli [ci skip] * add more references for reviewer-assemblies [ci skip] * add download script [ci skip] * dev iteration [ci skip] * use baseline java8 for orthoani [ci skip] * add orthoani util modules [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * update the hardware req for trimmomatic [ci skip] * add ggdc results [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * restore spades in favor of util process for filtering [ci skip] * add post-spades utils [ci skip] * add post-spades utils [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * make fastgrep executable [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * test with latest checkm process [ci skip] * retry with 1.1.8 checkm and reduced tree [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * dev iteration [ci skip] * regenrate the ggdc results [ci skip] * add params and orthoani subworkflow [ci skip] * use a custom container [ci skip] * use lower resources [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add raxml [ci skip] * add orthofinder [ci skip] * add orthofinder [ci skip] * add orthofinder [ci skip] * add orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthofinder [ci skip] * iterate on orthoani [ci skip]
Publication release
v1.4.0 tweak reamde
v1.3.0
add edson's user name
Update the pipeline name.
v1.2.1 publish the orthoani result separately
Finishing touches for the workflow stable release
v1.2-2021.05 Add readme
Improved documentation
Finishing touches to the workflow by Davi (#1) * Add a task file * [Suggestion] Add stubs to process (#2) * adding stubs to all modules * creating a bash script to generate mock data * adding stub_params and renaming mock data * changes following PR review * fixing typo on stub_params * adding last touches as requested on PR comments * [Suggestion] README with DAG file (#3) * adding stubs to all modules * creating a bash script to generate mock data * adding stub_params and renaming mock data * changes following PR review * fixing typo on stub_params * adding last touches as requested on PR comments * adding dag.dot and dag.png as resource to use later * Updating README * fixing typo on pipeline name * removing dag.dot * accepting modifications from pull request #3 * [Suggestion] Updating config files for Compute environments (#4) * adding stubs to all modules * creating a bash script to generate mock data * adding stub_params and renaming mock data * changes following PR review * fixing typo on stub_params * adding last touches as requested on PR comments * adding dag.dot and dag.png as resource to use later * Adding process configuration to nextflow.config profile * creating a standard profile and removing directives from modules * scratching profiles * renoving uncicler from google life science profile * removing configs from main and adding to folder * adding aws, gcp and azure configurations * adding aws access and secret key * changing nextflow.config * Changing azure profile name * using includeConfig to create profiles * removing dag.dot * adding local and standard profiles with process settings * removing local profile and fixing typo * [Suggestion] README with DAG file (#3) * adding stubs to all modules * creating a bash script to generate mock data * adding stub_params and renaming mock data * changes following PR review * fixing typo on stub_params * adding last touches as requested on PR comments * adding dag.dot and dag.png as resource to use later * Updating README * fixing typo on pipeline name * removing dag.dot * accepting modifications from pull request #3 * adding dag.dot and dag.png as resource to use later * Revert commits This reverts commit 14c4a96bea33bace100843d7398ef48643125da8. * Tweak readme * Further tweaks * Update the version Co-authored-by: Mxrcon <[email protected]>
Completed the first iteration of the analysis
v1.0-2021.04.1 Add errorstrategy