nf-core · jfy133 · Aug 24, 2021 · Apr 30, 2021 · May 3, 2021 · May 3, 2021
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -70,14 +70,13 @@ If you wish to contribute a new step, please use the following coding standards:
 3. Define the output channel if needed (see below).
 4. Add any new flags/options to `nextflow.config` with a default (see below).
 5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
-6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
-7. Add sanity checks for all relevant parameters.
-8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
-9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yaml`.
-11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+6. Add sanity checks for all relevant parameters.
+7. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
+8. Do local tests that the new code works properly and as expected.
+9. Add a new test command in `.github/workflow/ci.yaml`.
+10. If applicable add a [MultiQC](https://https://multiqc.info/) module.
+11. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
+12. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
 
 ### Default values
 

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -153,6 +153,9 @@ jobs:
       - name: GENOTYPING_ANGSD Test running ANGSD genotype likelihood calculation
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --run_genotyping --genotyping_tool 'angsd'
+      - name: GENOTYPING_BCFTOOLS Test running FreeBayes with bcftools stats turned on
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'freebayes' --run_bcftools_stats
       - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,12 +7,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
+- [#317](https://github.com/nf-core/eager/issues/317) Added bcftools stats for general genotyping statistics of VCF files
 - [#651](https://github.com/nf-core/eager/issues/651) - Adds removal of adapters specified in an AdapterRemoval adapter list file
-- [#769](https://github.com/nf-core/eager/issues/769) - Adds lc_extrap mode to preseq (requested by @roberta-davidson)
 - [#642](https://github.com/nf-core/eager/issues/642) and [#431](https://github.com/nf-core/eager/issues/431) adds post-adapter removal barcode/fastq trimming
+- [#769](https://github.com/nf-core/eager/issues/769) - Adds lc_extrap mode to preseq (requested by @roberta-davidson)
 
 ### `Fixed`
 
+- Fixed some missing or incorrectly reported software versions
 - [#771](https://github.com/nf-core/eager/issues/771) Remove legacy code
 - Improved output documentation for MultiQC general stats table (thanks to @KathrinNaegele and @esalmela)
 - Improved output documentation for BowTie2 (thanks to @isinaltinkaya)

diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -25,6 +25,7 @@ run_modules:
     - samtools
     - sexdeterrmine
     - hops
+    - bcftools
 
 extra_fn_clean_exts:
     - '_fastp'
@@ -93,6 +94,7 @@ top_modules:
     - 'mtnucratio'
     - 'qualimap'
     - 'sexdeterrmine'
+    - 'bcftools'
     - 'multivcfanalyzer':
        path_filters:
            - '*MultiVCFAnalyzer.json'

diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
@@ -37,7 +37,8 @@
     'kraken':['v_kraken.txt', r"Kraken version (\S+)"],
     'eigenstrat_snp_coverage':['v_eigenstrat_snp_coverage.txt',r"(\S+)"],
     'mapDamage2':['v_mapdamage.txt',r"(\S+)"],
-    'bbduk':['v_bbduk.txt',r"(.*)"]
+    'bbduk':['v_bbduk.txt',r"(.*)"],
+    'bcftools':['v_bcftools.txt',r"(\S+)"]
 }
 
 results = OrderedDict()
@@ -75,6 +76,7 @@
 results['eigenstrat_snp_coverage'] = '<span style="color:#999999;\">N/A</span>'
 results['mapDamage2'] = '<span style="color:#999999;\">N/A</span>'
 results['bbduk'] = '<span style="color:#999999;\">N/A</span>'
+results['bcftools'] = '<span style="color:#999999;\">N/A</span>'
 
 # Search each file using its regex
 for k, v in regexes.items():