# HG changeset patch
# User rliterman
# Date 1733419962 18000
# Node ID 6f4e6377ba64780ec0f2de289b732a5d3635d25a
# Parent a129538349168bb5b7415f19bc2aaa485bea93d1
"planemo upload"
diff -r a12953834916 -r 6f4e6377ba64 CSP2/.github/workflows/build-docker.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/.github/workflows/build-docker.yml Thu Dec 05 12:32:42 2024 -0500
@@ -0,0 +1,34 @@
+name: docker-build
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ docker:
+ runs-on: ubuntu-latest
+ steps:
+ -
+ name: Set up QEMU
+ uses: docker/setup-qemu-action@v3
+ -
+ name: Set up Docker Buildx
+ uses: docker/setup-buildx-action@v3
+ -
+ name: Login to Docker Hub
+ uses: docker/login-action@v3
+ with:
+ username: ${{ secrets.DOCKERHUB_USERNAME }}
+ password: ${{ secrets.DOCKERHUB_TOKEN }}
+ -
+ name: Build and push
+ uses: docker/build-push-action@v6
+ with:
+ file: docker/Dockerfile
+ platforms: linux/amd64
+ target: release
+ build-args: |
+ VERSION=${{ github.ref_name }}
+ CSP2_BRANCH=${{ github.ref_name }}
+ push: true
+ tags: cfsanbiostatistics/csp2:latest,cfsanbiostatistics/csp2:${{ github.ref_name }}
diff -r a12953834916 -r 6f4e6377ba64 CSP2/.gitignore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/.gitignore Thu Dec 05 12:32:42 2024 -0500
@@ -0,0 +1,211 @@
+# Created by https://www.toptal.com/developers/gitignore/api/python,visualstudiocode,virtualenv
+# Edit at https://www.toptal.com/developers/gitignore?templates=python,visualstudiocode,virtualenv
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# For a library or package, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+# This is especially recommended for binary packages to ensure reproducibility, and is more
+# commonly ignored for libraries.
+# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+# in version control.
+# https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+# and can be added to the global gitignore or merged into this file. For a more nuclear
+# option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+### VirtualEnv ###
+# Virtualenv
+# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
+[Bb]in
+[Ii]nclude
+[Ll]ib
+[Ll]ib64
+[Ll]ocal
+[Ss]cripts
+pyvenv.cfg
+pip-selfcheck.json
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+# End of https://www.toptal.com/developers/gitignore/api/python,visualstudiocode,virtualenv
+
+#Nextflow
+.nextflow*
+work/
\ No newline at end of file
diff -r a12953834916 -r 6f4e6377ba64 CSP2/conf/profiles.config
--- a/CSP2/conf/profiles.config Thu Dec 05 10:47:01 2024 -0500
+++ b/CSP2/conf/profiles.config Thu Dec 05 12:32:42 2024 -0500
@@ -79,13 +79,13 @@
params.trim_name = ""
}
- csp2_galaxy {
+ csp2_galaxy1 {
conda.enabled = true
conda.useMicromamba = true
conda.cacheDir = "${projectDir}/CSP2_env"
process.conda = "${projectDir}/conf/CSP2.yaml"
- process.queue = "q8cpu"
+ process.queue = "ondemand-small"
executor.$slurm.exitReadTimeout = 120000
@@ -99,4 +99,25 @@
params.mash_module = ""
params.trim_name = ""
}
+
+ csp2_galaxy2 {
+ conda.enabled = true
+ conda.useMicromamba = true
+ conda.cacheDir = "${projectDir}/CSP2_env"
+ process.conda = "${projectDir}/conf/CSP2.yaml"
+
+ process.queue = "q8cpu"
+
+ executor.$slurm.exitReadTimeout = 120000
+
+ process.executor = 'slurm'
+ params.cores = 8
+ params.python_module = ""
+ params.mummer_module = ""
+ params.skesa_module = ""
+ params.bedtools_module = ""
+ params.bbtools_module = ""
+ params.mash_module = ""
+ params.trim_name = ""
+ }
}
diff -r a12953834916 -r 6f4e6377ba64 csp2_screen.xml
--- a/csp2_screen.xml Thu Dec 05 10:47:01 2024 -0500
+++ b/csp2_screen.xml Thu Dec 05 12:32:42 2024 -0500
@@ -57,7 +57,13 @@
export REF_ID_ARG="";
fi;
-nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 2 --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
+if [[ "$ondemand" == "true" ]]; then
+ export PROFILE_ARG="-profile csp2_galaxy1";
+else
+ export PROFILE_ARG="-profile csp2_galaxy2";
+fi;
+
+nextflow run ${__tool_directory__}/CSP2/CSP2.nf \$PROFILE_ARG --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
zip -r CSP2_Output.zip CSP2_Screen_Output;
]]>
@@ -78,6 +84,7 @@
+
diff -r a12953834916 -r 6f4e6377ba64 csp2_snp.xml
--- a/csp2_snp.xml Thu Dec 05 10:47:01 2024 -0500
+++ b/csp2_snp.xml Thu Dec 05 12:32:42 2024 -0500
@@ -63,7 +63,13 @@
export RESCUE_ARG="";
fi;
-nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 2 --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG \$RESCUE_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --max_missing $max_missing --n_ref $n_ref --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
+if [[ "$ondemand" == "true" ]]; then
+ export PROFILE_ARG="-profile csp2_galaxy1";
+else
+ export PROFILE_ARG="-profile csp2_galaxy2";
+fi;
+
+nextflow run ${__tool_directory__}/CSP2/CSP2.nf \$PROFILE_ARG --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG \$RESCUE_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --max_missing $max_missing --n_ref $n_ref --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
zip -r CSP2_Output.zip CSP2_SNP_Output;
]]>
@@ -87,7 +93,7 @@
-
+