5i6\ddlmZmZmZmZmZmZddlZddlZddl m Z  ddZ ddZ y) )get_template_dirget_source_file_nameget_resources_subpathis_importer_jobget_regional_optionsget_resources_dir_nameN)TOOLKIT_VERSIONc|g}ttjjt t dd5}t j|}ddd|dz|d<t|dd<t|}||dk(rd}||d <||d <||d <t||||||d <t|d d<tjjd tsd|d d<|S#1swYxYw)ai :param custom_inputs: Custom inputs that will be used in the created Nextflow pipeline. :type custom_inputs: list :param resources_dir: Directory with all resources needed for the Nextflow pipeline. Usually directory with user's Nextflow files. :type resources_dir: str or Path :param region: The name of the region in which the applet will be built. :type region: str :param profile: Custom Nextflow profile. More profiles can be provided by using comma separated string (without whitespaces). :type profile: str :param cache_docker: Perform pipeline analysis and cache the detected docker images on the platform :type cache_docker: boolean :param nextflow_pipeline_params: Custom Nextflow pipeline parameters :type nextflow_pipeline_params: string Creates Nextflow dxapp.json from the Nextflow dxapp.json template Nz dxapp.jsonr inputSpecrunSpecfilezNextflow pipelinenametitlesummaryregionalOptionsdetailsdxpyBuildVersion DX_JOB_IDlocal repository)openospathjoinstrrjsonloadrrrr environgetr) custom_inputs resources_dirregionprofile cache_dockernextflow_pipeline_paramsfdxapprs /home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/nextflow/nextflow_templates.pyget_nextflow_dxappr, s 0 bggll3/12LA3 G1 ! &{);;E+35E)V "- 0D |trz"E&ME'NE)3FM7T`bz{E ,;E)'( zz~~k"*/2C)0i& L%s C--C6c|g}ttjjt t t d5}|j}dddd}d}|D]Y}d|dz}|jddk(rd|dz}|d j|dz }|d j|d|d|z}[|rd j|nd} jd |}|jd | }|jd|}|jdt}|jdt|}|S#1swYxYw)a :param custom_inputs: Custom inputs (as configured in nextflow_schema.json) that will be used in created runtime configuration and runtime params argument :type custom_inputs: list :param profile: Custom Nextflow profile to be used when running a Nextflow pipeline, for more information visit https://www.nextflow.io/docs/latest/config.html#config-profiles :type profile: string :param resources_dir: Directory with all source files needed to build an applet. Can be an absolute or a relative path. :type resources_dir: str or Path :returns: String containing the whole source file of an applet. :rtype: string Creates Nextflow source file from the Nextflow source file template Nr rz${%s}rclassrzrdx://${DX_WORKSPACE_ID}:/$(echo ${%s} | jq .[$dnanexus_link] -r | xargs -I {} dx describe {} --json | jq -r .name)z --except {} za if [ -n "${}" ]; then applet_runtime_inputs+=(--{} "{}") fi z -profile {}z@@APPLET_RUNTIME_PARAMS@@z@@PROFILE_ARG@@z@@EXCLUDE_INPUT_DOWNLOAD@@z@@DXPY_BUILD_VERSION@@z@@RESOURCES_SUBPATH@@) rrrrrrrreadr"formatreplacer r) r#r&r$r)srcexclude_input_downloadapplet_runtime_paramsivalue profile_args r+get_nextflow_srcr89sh bggll3/124H4JKS QUVffh   01V9% 55>V #IfIE "n&;&;AfI&F F "!69  F1V9ai / !0 04;-&&w/K ++13H IC ++' 5C ++24J KC ++. @C ++-/ > @C J7s EE )Nrz aws:us-east-1rFr)NNN) nextflow_utilsrrrrrrrrdxpyr r,r8r+r=s9\\ !# ,^*r<