Merge pull request #6 from CCBR/bwa-mem

fix md5sums & document automated test yaml creation

.github/CONTRIBUTING.md

@@ -1,21 +1,31 @@
 # Contributing to nf-modules
 
-TODO -- describe gitflow, require PRs...
+## Unit tests
 
-## Use pre-commit hooks
+Once you've written or updated a module under `modules/CCBR/[module-name]` and
+a test workflow under `tests/modules/CCBR/[module-name]`,
+then use nf-core tools to automatically create a test YAML file with:
+
+```sh
+nf-core modules create-test-yml [module-name] --run-tests --force --no-prompts
+```
+
+Add the module to `tests/config/pytest_modules.yml`
+
+Run the tests with:
+
+```sh
+PROFILE=docker nf-core modules test [module-name] --no-prompts
+```
+
+## Pre-commit hooks
 
 Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.
 
 Install [pre-commit](https://pre-commit.com/#installation) if you haven't already,
 then run `pre-commit install` to install the hooks specified in `.pre-commit-config.yaml`.
 Pre-commit will run the hooks every time you commit.
 
-## Versions
-
-Increment the version number following semantic versioning[^1] in the `VERSION` file.
-
-[^1]: semantic versioning guidelines https://semver.org/
-
 ## Changelog
 
 Keep the changelog up to date with all notable changes in `CHANGELOG.md`[^2].

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,6 +18,6 @@ when referring to the issue.
 (~Strikethrough~ any points that are not applicable.)
 
 - [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
-- ~[ ] Write unit tests for any new features, bug fixes, or other code changes.~ _testing framework not yet implemented_
-- ~[ ] Update docs if there are any API changes.~ _on hold until before public release_
+- [ ] Write unit tests for any new features, bug fixes, or other code changes.
+- [ ] Update docs if there are any API changes.
 - [ ] Update `CHANGELOG.md` with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

README.md

@@ -30,7 +30,7 @@ Come across a **bug**? Open an [issue](https://github.com/CCBR/nf-modules/issues
 
 Have a **question**? Ask it in [discussions](https://github.com/CCBR/nf-modules/discussions).
 
-Want to **contribute** to this project? Check out the [contributing guidelines](docs/CONTRIBUTING.md).
+Want to **contribute** to this project? Check out the [contributing guidelines](.github/CONTRIBUTING.md).
 
 ## References
 

modules/CCBR/bwa/mem/main.nf

@@ -39,6 +39,7 @@ process BWA_MEM {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
     stub:
     """
     touch ${meta.id}.bam versions.yml

tests/modules/CCBR/bwa/mem/main.nf

@@ -43,43 +43,3 @@ workflow test_bwa_mem_paired_end {
     BWA_INDEX ( fasta )
     BWA_MEM ( input, BWA_INDEX.out.index )
 }
-
-//
-// Test with stub pairedend
-//
-workflow test_bwa_mem_paired_end_stub {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = [
-        [id: 'test'],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    BWA_INDEX ( fasta )
-    BWA_MEM ( input, BWA_INDEX.out.index )
-}
-
-
-//
-// Test with single-end data stub
-//
-workflow test_bwa_mem_single_end_stub {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = [
-        [id: 'test'],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    BWA_INDEX ( fasta )
-    BWA_MEM ( input, BWA_INDEX.out.index )
-}

tests/modules/CCBR/bwa/mem/test.yml

@@ -1,8 +1,8 @@
 - name: bwa mem test_bwa_mem_single_end
   command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config
   tags:
-    - bwa
     - bwa/mem
+    - bwa
   files:
     - path: output/bwa/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
@@ -15,34 +15,14 @@
     - path: output/bwa/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: fe5a30103b245d81a8d37d6144794f5
+      md5sum: fe5a30103b245d81a8d37d6144794f56
     - path: output/bwa/versions.yml
 
 - name: bwa mem test_bwa_mem_paired_end
   command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_paired_end -c ./tests/config/nextflow.config
   tags:
-    - bwa
     - bwa/mem
-  files:
-    - path: output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: output/bwa/test.bam
-      md5sum: 06b8e7424d97add946ddb07e55f12962
-    - path: output/bwa/versions.yml
-
-- name: bwa mem test_bwa_mem_paired_end_stub
-  command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_paired_end_stub -c ./tests/config/nextflow.config
-  tags:
     - bwa
-    - bwa/mem
   files:
     - path: output/bwa/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
@@ -57,23 +37,3 @@
     - path: output/bwa/test.bam
       md5sum: 06b8e7424d97add946ddb07e55f12962
     - path: output/bwa/versions.yml
-
-- name: bwa mem test_bwa_mem_single_end_stub
-  command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_single_end_stub -c ./tests/config/nextflow.config
-  tags:
-    - bwa
-    - bwa/mem
-  files:
-    - path: output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: output/bwa/test.bam
-      md5sum: fe5a30103b245d81a8d37d6144794f56
-    - path: output/bwa/versions.yml