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+# Quick guide to running ResFinder with Cromwell
+
+### Disclaimer
+Support is not offered for running Cromwell and no files in this directory is
+guaranteed to work. These files were uploaded as inspiration. Please do not
+report issues relating to this directory.
+
+## Prepare input files
+
+Two input files are needed:
+
+1. input_data.tsv
+2. input.json
+
+Templates can be found in the ResFinder directory scripts/wdl.
+
+### input_data.tsv
+Tab separated file. Should contain columns in the following order:
+
+1. Absolute path to fasta/fastq file 1
+2. Absolute path to fastq file 2 (Can be empty, but must exist)
+3. Species
+4. Type of data, must be one of: assembly, paired
+
+Each row should contain a single sample.
+
+#### Species
+If species cannot be provided put "other" (cases sensitive).
+
+#### Type of data
+
+* assembly: Fasta file containing contigs from a de novo assembly.
+* paired: Couple of fastq files containing read data for foward and reverse
+reads.
+* single: **Not implemented** Read data from single-end sequencing.
+
+
+#### Example
+```
+
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_01_1.fq	/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_01_2.fq	Escherichia	coli	paired
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_05_1.fq	/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_05_2.fq	Escherichia	coli	paired
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_09a_1.fq	/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_09a_2.fq	Escherichia	coli	paired
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_09b_1.fq	/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_09b_2.fq	Escherichia	coli	paired
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_01.fa		Escherichia	coli	assembly
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_02.fa		Escherichia	coli	assembly
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_03.fa		Escherichia	coli	assembly
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_05.fa		Escherichia	coli	assembly
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_09a.fa		Escherichia	coli	assembly
+/home/projects/cge/apps/resfinder/resfinder/tests/data/test_isolate_09b.fa		Escherichia	coli	assembly
+
+```
+
+### input.json
+JSON formatted file containing input and output information.
+
+The file should consist of a single dict/hash/map with the following keys:
+
+* Resistance.inputSamplesFile: Absolute path to input_data.tsv
+* Resistance.outputDir: Absolute path to output directory.
+* Resistance.geneCov: Fraction of gene coverage needed for resistance gene hits.
+* Resistance.geneID: Fraction of nucleotide identity needed in resistance gene
+hits.
+* Resistance.pointCov: Fraction of gene coverage needed for point mutation gene
+hits.
+* Resistance.pointID: Fraction of nucleotide identity needed in point mutation gene
+hits.
+
+If running on Computerome and are using the input.json template, you probably
+won't need to change the following:
+
+* Resistance.python: Path to python3 interpreter.
+* Resistance.kma: Path to kma application.
+* Resistance.blastn: Path to blastn application.
+* Resistance.resfinder: Path to run_resfinder.py.
+* Resistance.resDB: Path to ResFinder database.
+* Resistance.pointDB: Path to PointFinder database
+
+The values should be the absolute path to the input_data.tsv and the desired
+output directory, respectively.
+
+#### Example
+
+```json
+
+{
+  "Resistance.inputSamplesFile": "/home/projects/cge/people/rkmo/delme/res_input.tsv",
+  "Resistance.outputDir": "/home/projects/cge/people/rkmo/delme/",
+  "Resistance.geneCov": 0.6,
+  "Resistance.geneID": 0.8,
+  "Resistance.pointCov": 0.6,
+  "Resistance.pointID": 0.8,
+  "Resistance.python": "python3",
+  "Resistance.kma": "/home/projects/cge/apps/resfinder/resfinder/cge/kma/kma",
+  "Resistance.blastn": "blastn",
+  "Resistance.resfinder": "/home/projects/cge/apps/resfinder/resfinder/run_resfinder.py",
+  "Resistance.resDB": "/home/projects/cge/apps/resfinder/resfinder/db_resfinder",
+  "Resistance.pointDB": "/home/projects/cge/apps/resfinder/resfinder/db_pointfinder"
+}
+
+```
+
+## Run Cromwell
+
+Cromwell needs JAVA to run. Load a valid JAVA module, for example:
+
+```bash
+
+module load openjdk/16
+
+```
+
+A Cromwell call looks like this:
+
+```bash
+
+java -Dconfig.file=<CONF> -jar <CROMWELL> run <WDL> --inputs <JSON>
+
+```
+
+### <CONF> and <CROMWELL>
+Computerome specific.
+
+* <CONF>: Path to Computerome configuration for Cromwell. You need to change
+this if you are not running Cromwell on Computerome. Computerome path:
+/home/projects/cge/apps/resfinder/resfinder/scripts/wdl/computerome.conf
+
+* <CROMWELL>: Path to Cronwell jar file in Computerome:
+/services/tools/cromwell/50/cromwell-50.jar
+
+### <WDL>
+ResFinder specific.
+
+* <WDL>: Path to wdl file that specifies how to run ResFinder. Path to
+resfinder.wdl on Computerome:
+/home/projects/cge/apps/resfinder/resfinder/scripts/wdl/resfinder.wdl
+
+### <JSON>
+User/Run specific
+
+Path to input.json. Specifies all the parameters for ResFinder (See above).
+
+### Run example
+
+```bash
+
+java -Dconfig.file=/home/projects/cge/apps/resfinder/resfinder/scripts/wdl/computerome.conf -jar /services/tools/cromwell/50/cromwell-50.jar run /home/projects/cge/apps/resfinder/resfinder/scripts/wdl/resfinder.wdl --inputs /home/projects/cge/apps/resfinder/resfinder/scripts/wdl/input.json
+
+```
+
+### Post run
+
+All ResFinder output will be located in the provided output directory.
+
+In the directory where you execute Cromwell the following two directories will
+also be created:
+
+* cromwell-executions
+* cromwell-workflow-logs
+
+They contain logging information and cached results.