diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index de8f4598..98343750 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -73,7 +73,8 @@ If you wish to contribute a new step, please use the following coding standards:
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test command in `.github/workflow/ci.yml`.
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
-10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+10. Update the tool references `assets/software_references.yml`.
+11. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
### Default values
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f1aa6311..dda988c8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -97,6 +97,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#506](https://github.com/genomic-medicine-sweden/nallo/pull/506) - Updated documentation
- [#507](https://github.com/genomic-medicine-sweden/nallo/pull/507) - Changed the default value of `ch_hgnc_ids` to allow running without `--filter_variants_hgnc_ids` introduced in [#496](https://github.com/genomic-medicine-sweden/nallo/pull/443)
- [#509](https://github.com/genomic-medicine-sweden/nallo/pull/509) - Updated documentation to fix mistakes
+- [#510](https://github.com/genomic-medicine-sweden/nallo/pull/510) - Changed the MultiQC methods description to update dynamically based on `ch_versions`
- [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed one `single_sample` to `sample` and one `multi_sample` to `family` output directories missed in [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502)
- [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed all `*_snv_*` to `*_snvs_*` for published output files to match `snvs`, `cnvs`, `svs` and `repeats`.
- [#513](https://github.com/genomic-medicine-sweden/nallo/pull/513) - Updated CITATIONS.md link in README
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 8c9c1c1b..d8195c2e 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -5,5 +5,14 @@ section_href: "https://github.com/genomic-medicine-sweden/nallo"
plot_type: "html"
data: |
Methods
- Data was processed using genomic-medicine-sweden/nallo v${workflow.manifest.version} ${doi_text} which uses uses code and infrastructure developed and maintained by the nf-core community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE) (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
+ Data was processed using genomic-medicine-sweden/nallo v${workflow.manifest.version} ${doi_text} which uses uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT licence (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:
+ ${workflow.commandLine}
+
+
Notes:
+
+ ${nodoi_text}
+ - The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
+ - You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
+
+
Tools used in the workflow included: ${items.join(', ')}.
"
+ } else if (description == 'bibliography') {
+ return " References
"
+ }
+}
+
+def citationBibliographyText(ch_versions, references_yaml, description) {
+ def yaml = new org.yaml.snakeyaml.Yaml()
+ def softwareReferences = yaml.load(references_yaml.text).tool
+
+ def unwantedReferences = ['genomic-medicine-sweden/nallo', 'Nextflow']
+ // These are not collected in ch_versions but should be referenced
+ baseTools = Channel.from(['nextflow', 'nf_core', 'bioconda', 'biocontainers', 'multiqc'])
+
+ ch_versions
+ .map { module_yaml -> extractSoftwareFromVersions(module_yaml) }
+ .flatten() // split multi-tool modules
+ .unique()
+ .filter { tool -> !unwantedReferences.contains(tool) }
+ .concat(baseTools)
+ .collect { tool ->
+ def toolDetails = softwareReferences[tool]
+ if (toolDetails == null) {
+ throw new IllegalStateException("Tool: '${tool}' not found in ${references_yaml}")
+ }
+ return toolDetails[description]
+ }
+ .sort()
+ .map { tools -> generateReferenceHTML(tools, description) }
+}
+
//
// Validate workflow skip combinations
//
diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
index ed3341c3..bc375a87 100644
--- a/tests/samplesheet.nf.test.snap
+++ b/tests/samplesheet.nf.test.snap
@@ -5,7 +5,7 @@
{
"ADD_FOUND_IN_TAG": {
"bcftools": 1.2,
- "busybox-awk": "1.36.1"
+ "busybox_awk": "1.36.1"
},
"ADD_MOST_SEVERE_CSQ": {
"add_most_severe_consequence": 1.0,
diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap
index 20d29438..ffc6d25c 100644
--- a/tests/samplesheet_multisample_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -5,7 +5,7 @@
{
"ADD_FOUND_IN_TAG": {
"bcftools": 1.2,
- "busybox-awk": "1.36.1"
+ "busybox_awk": "1.36.1"
},
"ADD_MOST_SEVERE_CSQ": {
"add_most_severe_consequence": 1.0,
diff --git a/tests/samplesheet_multisample_ont_bam.nf.test.snap b/tests/samplesheet_multisample_ont_bam.nf.test.snap
index c3bfc566..425e7c48 100644
--- a/tests/samplesheet_multisample_ont_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_ont_bam.nf.test.snap
@@ -5,7 +5,7 @@
{
"ADD_FOUND_IN_TAG": {
"bcftools": 1.2,
- "busybox-awk": "1.36.1"
+ "busybox_awk": "1.36.1"
},
"ADD_MOST_SEVERE_CSQ": {
"add_most_severe_consequence": 1.0,
diff --git a/workflows/nallo.nf b/workflows/nallo.nf
index 799789ab..4da63a3b 100644
--- a/workflows/nallo.nf
+++ b/workflows/nallo.nf
@@ -59,6 +59,7 @@ include { paramsSummaryMap } from 'plugin/nf-sc
include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nallo_pipeline'
+include { citationBibliographyText } from '../subworkflows/local/utils_nfcore_nallo_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -639,15 +640,29 @@ workflow NALLO {
ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
file(params.multiqc_methods_description, checkIfExists: true) :
file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
- ch_methods_description = Channel.value(
- methodsDescriptionText(ch_multiqc_custom_methods_description))
-
+ ch_methods_description = Channel.of(
+ methodsDescriptionText(ch_multiqc_custom_methods_description)
+ )
+ ch_methods_description_citation = citationBibliographyText(
+ ch_versions,
+ file("$projectDir/assets/software_references.yml"),
+ 'citation'
+ )
+ ch_methods_description_bibliography = citationBibliographyText(
+ ch_versions,
+ file("$projectDir/assets/software_references.yml"),
+ 'bibliography'
+ )
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(
- ch_methods_description.collectFile(
- name: 'methods_description_mqc.yaml',
- sort: true
- )
+ ch_methods_description
+ .concat(ch_methods_description_citation)
+ .concat(ch_methods_description_bibliography)
+ .flatten()
+ .collectFile(
+ name: 'methods_description_mqc.yaml',
+ sort: false // preserve order for correct yaml structure
+ )
)
MULTIQC (