Cytosine report test

docs/usage.md

@@ -88,6 +88,24 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
+## Parameters
+
+Check out the full list of parameters required, available for multiple aligners on [nf-core/methylseq pipeline parameters page](https://nf-co.re/methylseq/2.8.0/parameters/).
+
+- [Input/output options](https://nf-co.re/methylseq/2.8.0/parameters/#input-output-options)
+- [Save intermediate files](https://nf-co.re/methylseq/2.8.0/parameters/#save-intermediate-files)
+- [Reference genome options](https://nf-co.re/methylseq/2.8.0/parameters/#reference-genome-options)
+- [Alignment options](https://nf-co.re/methylseq/2.8.0/parameters/#alignment-options)
+- [Special library types](https://nf-co.re/methylseq/2.8.0/parameters/#special-library-types)
+- [Adapter Trimming](https://nf-co.re/methylseq/2.8.0/parameters/#adapter-trimming)
+- [Bismark options](https://nf-co.re/methylseq/2.8.0/parameters/#bismark-options)
+- [bwa-meth options](https://nf-co.re/methylseq/2.8.0/parameters/#bwa-meth-options)
+- [Qualimap Options](https://nf-co.re/methylseq/2.8.0/parameters/#bwa-meth-options)
+- [Skip pipeline steps](https://nf-co.re/methylseq/2.8.0/parameters/#skip-pipeline-steps)
+- [Run pipeline steps](https://nf-co.re/methylseq/2.8.0/parameters/#Run-pipeline-steps)
+
+> It is mandatory to provide `--fasta` along with `--bismark_index`/`--bwameth_index` parameters
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:
@@ -139,7 +157,10 @@ For example, users working with unfinished genomes containing tens or even hundr
 
 To bypass this limitation, the `--scaffolds` option can be added as an additional `ext.args` in `conf/modules/bismark_methylationextractor.config`. This prevents methylation calls from being pre-sorted into individual chromosome files. Instead, all input files are temporarily merged into a single file (unless there is only one file), which is then sorted by both chromosome and position using the Unix sort command.
 
-> For a detailed list of different options available, please refer to the official [Bismark](https://felixkrueger.github.io/Bismark/options/genome_preparation/) and [bwa-meth](https://github.com/brentp/bwa-meth) documentation.
+For a detailed list of different options available, please refer to the official docs of:
+
+- [Bismark](https://felixkrueger.github.io/Bismark/options/genome_preparation/)
+- [bwa-meth](https://github.com/brentp/bwa-meth)
 
 ### Running the `test` profile
 

tests/bismark_cytosine_report.nf.test

@@ -0,0 +1,41 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+    config "./nextflow.config"
+    tag "cpu"
+
+    test("Params: bismark | cytosine_report") {
+        when {
+            params {
+                cytosine_report = true
+                outdir          = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"),
+                    // All stable path name
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+}