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Merge branch 'wdl-1-2-directory' into 'master'
Add directory input handling for Bruker data file input to WDL See merge request mass-spectrometry/enviroms!14
2 parents f7b29d6 + d7185d6 commit 85fb3da

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‎.github/workflows/di_workflow_tests.yaml‎

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run: |
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make docker-build-local
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- name: Run Bruker di WDL with local Docker Image based on Dockerfile
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run: |
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miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_local_docker_bruker.json --verbose --no-cache --copy-input-files
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- name: Run Bruker di WDL with pushed Docker Image
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run: |
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make wdl-run-di-bruker
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- name: Run di WDL with local Docker Image based on Dockerfile
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run: |
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miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files

‎Makefile‎

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@make docker-build-local
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miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files
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wdl-run-di-bruker :
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miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_bruker.json --verbose --no-cache --copy-input-files
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wdl-run-di-bruker-local :
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@make docker-build-local
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miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_local_docker_bruker.json --verbose --no-cache --copy-input-files
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wdl-run-lc :
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miniwdl run wdl/lc_fticr_ms.wdl -i wdl/lc_fticr_wdl_input.json --verbose --no-cache --copy-input-files

‎README.md‎

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```
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For Direct Infusion Workflow:
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_Note that for the direct infusion workflow, the WDL file used depends on the instrument/output file type. Use "Bruker" WDL for .d files and general WDL for ".raw" files._
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```bash
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miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
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miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
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```
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For Liquid Chromatography Workflow:
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```bash

‎wdl/di_fticr_ms.wdl‎

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version 1.0
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version 1.2
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workflow fticrmsNOM {
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input {

‎wdl/di_fticr_ms_bruker.wdl‎

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version 1.2
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workflow fticrmsNOM {
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input {
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String? docker_image # Optional input for Docker image
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}
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call runDirectInfusion {
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input:
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docker_image = docker_image
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}
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output {
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String out = runDirectInfusion.out
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Array[File] output_files = runDirectInfusion.output_files
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Array[File] van_krevelen_plots = runDirectInfusion.van_krevelen_plots
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Array[File] dbe_vs_c_plots = runDirectInfusion.dbe_vs_c_plots
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Array[File] ms_class_plots = runDirectInfusion.ms_class_plots
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Array[File] mz_error_class_plots = runDirectInfusion.mz_error_class_plots
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Array[File] qc_plots = runDirectInfusion.qc_plots
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}
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}
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task runDirectInfusion {
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input {
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Array[Directory] file_paths
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String output_directory
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String output_type
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File corems_toml_path
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String polarity
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Int raw_file_start_scan
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Int raw_file_final_scan
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Boolean is_centroid
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File calibration_ref_file_path
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Boolean calibrate
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Boolean batch_calibrate
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Boolean plot_mz_error
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Boolean plot_ms_assigned_unassigned
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Boolean plot_c_dbe
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Boolean plot_van_krevelen
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Boolean plot_ms_classes
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Boolean plot_mz_error_classes
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Boolean plot_qc
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Int jobs_count = 1
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String? docker_image
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}
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command {
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enviroMS run_di_wdl \
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${sep=',' file_paths} \
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${output_directory} \
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${output_type} \
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${corems_toml_path} \
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${polarity} \
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${raw_file_start_scan} \
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${raw_file_final_scan} \
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${is_centroid} \
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${calibration_ref_file_path} \
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-c ${calibrate} \
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-bc ${batch_calibrate} \
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-e ${plot_mz_error} \
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-a ${plot_ms_assigned_unassigned} \
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-cb ${plot_c_dbe} \
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-vk ${plot_van_krevelen} \
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-mc ${plot_ms_classes} \
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-ec ${plot_mz_error_classes} \
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-qc ${plot_qc} \
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--jobs ${jobs_count}
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}
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output {
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String out = read_string(stdout())
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Array[File] output_files = glob('${output_directory}/**/*.*')
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Array[File] van_krevelen_plots = glob('${output_directory}/**/van_krevelen/*.*')
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Array[File] dbe_vs_c_plots = glob('${output_directory}/**/dbe_vs_c/*.*')
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Array[File] ms_class_plots = glob('${output_directory}/**/ms_class/*.*')
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Array[File] mz_error_class_plots = glob('${output_directory}/**/mz_error_class/*.*')
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Array[File] qc_plots = glob('${output_directory}/**/qc_plots/*.*')
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}
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runtime {
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docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/enviroms:5.1.0'}"
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}
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}

‎wdl/di_fticr_wdl_input_bruker.json‎

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{
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"fticrmsNOM.runDirectInfusion.file_paths": [
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"data/raw_data/NEG_ESI_SRFA_Auto.d"
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],
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"fticrmsNOM.runDirectInfusion.output_directory": "output",
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"fticrmsNOM.runDirectInfusion.output_type": "csv",
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"fticrmsNOM.runDirectInfusion.calibrate": true,
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"fticrmsNOM.runDirectInfusion.batch_calibrate": true,
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"fticrmsNOM.runDirectInfusion.calibration_ref_file_path": "./data/reference/SRFA.ref",
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"fticrmsNOM.runDirectInfusion.corems_toml_path": "./configuration/di_corems.toml",
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"fticrmsNOM.runDirectInfusion.polarity": "negative",
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"fticrmsNOM.runDirectInfusion.is_centroid": true,
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"fticrmsNOM.runDirectInfusion.raw_file_start_scan": 1,
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"fticrmsNOM.runDirectInfusion.raw_file_final_scan": 7,
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"fticrmsNOM.runDirectInfusion.plot_mz_error": false,
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"fticrmsNOM.runDirectInfusion.plot_ms_assigned_unassigned": false,
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"fticrmsNOM.runDirectInfusion.plot_c_dbe": false,
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"fticrmsNOM.runDirectInfusion.plot_van_krevelen": false,
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"fticrmsNOM.runDirectInfusion.plot_ms_classes": false,
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"fticrmsNOM.runDirectInfusion.plot_mz_error_classes": false,
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"fticrmsNOM.runDirectInfusion.plot_qc": true
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}
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‎wdl/di_fticr_wdl_input_local_docker_bruker.json‎

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{
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"fticrmsNOM.docker_image": "local-enviroms:latest",
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"fticrmsNOM.runDirectInfusion.file_paths": [
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"data/raw_data/NEG_ESI_SRFA_Auto.d"
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],
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"fticrmsNOM.runDirectInfusion.output_directory": "output",
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"fticrmsNOM.runDirectInfusion.output_type": "csv",
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"fticrmsNOM.runDirectInfusion.calibrate": true,
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"fticrmsNOM.runDirectInfusion.batch_calibrate": true,
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"fticrmsNOM.runDirectInfusion.calibration_ref_file_path": "./data/reference/SRFA.ref",
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"fticrmsNOM.runDirectInfusion.corems_toml_path": "./configuration/di_corems.toml",
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"fticrmsNOM.runDirectInfusion.polarity": "negative",
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"fticrmsNOM.runDirectInfusion.is_centroid": true,
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"fticrmsNOM.runDirectInfusion.raw_file_start_scan": 1,
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"fticrmsNOM.runDirectInfusion.raw_file_final_scan": 7,
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"fticrmsNOM.runDirectInfusion.plot_mz_error": false,
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"fticrmsNOM.runDirectInfusion.plot_ms_assigned_unassigned": false,
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"fticrmsNOM.runDirectInfusion.plot_c_dbe": false,
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"fticrmsNOM.runDirectInfusion.plot_van_krevelen": false,
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"fticrmsNOM.runDirectInfusion.plot_ms_classes": false,
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"fticrmsNOM.runDirectInfusion.plot_mz_error_classes": false,
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"fticrmsNOM.runDirectInfusion.plot_qc": true
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}

‎wdl/lc_fticr_ms.wdl‎

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version 1.0
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version 1.2
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workflow lc_ft_icr_ms {
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input {

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