Release 1.2.0

.github/CONTRIBUTING.md

@@ -116,4 +116,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

.github/workflows/awsfulltest.yml

@@ -14,18 +14,24 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
+        # Add full size test data (but still relatively small datasets for few samples)
+        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nanostring/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nanostring/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -12,18 +12,21 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nanostring/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nanostring/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/ci.yml

@@ -38,7 +38,6 @@ jobs:
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
       - name: Run pipeline with test data and gene scores
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_scores,docker --outdir ./results

.gitpod.yml

@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

CHANGELOG.md

@@ -3,6 +3,30 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.2.0 - 2023-08-24 - Nanometre
+
+### `Added`
+
+- [#48](https://github.com/nf-core/nanostring/pull/48) - Allow users to specify id column for heatmap [#39](https://github.com/nf-core/nanostring/issues/39)
+- [#46](https://github.com/nf-core/nanostring/pull/46) - Update to nf-core template `2.9`
+- [#42](https://github.com/nf-core/nanostring/pull/42) - Allow users to specify normalization method: `GEO` (default) or `GLM`
+
+### `Fixed`
+
+- [#51](https://github.com/nf-core/nanostring/pull/51) - Prevent HK-normalization while loading counts
+- [#51](https://github.com/nf-core/nanostring/pull/51) - Use provided normalization method for Non-HK-normalized counts
+- [#46](https://github.com/nf-core/nanostring/pull/46) - Publish `NACHO` QC reports [#44](https://github.com/nf-core/nanostring/issues/44)
+- [#47](https://github.com/nf-core/nanostring/pull/47) - Update `NACHO` R package including bug fix [#45](https://github.com/nf-core/nanostring/issues/45)
+- [#47](https://github.com/nf-core/nanostring/pull/47) - Set correct `conda` environment for `COMPUTE_GENE_SCORES` process
+
+### `Dependencies`
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `nacho`    | 2.0.4       | 2.0.5       |
+
+### `Deprecated`
+
 ## v1.1.1 - 2023-06-23
 
 ### `Added`

CITATIONS.md

@@ -40,5 +40,8 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

README.md

@@ -58,22 +58,22 @@ nextflow run nf-core/nanostring \
 > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
 > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
-For more details, please refer to the [usage documentation](https://nf-co.re/nanostring/usage) and the [parameter documentation](https://nf-co.re/nanostring/parameters).
+For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/nanostring/usage) and the [parameter documentation](https://nf-co.re/nanostring/parameters).
 
 ## Pipeline output
 
-To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/nanostring/results) tab on the nf-core website pipeline page.
+To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/nanostring/results) tab on the nf-core website pipeline page.
 For more details about the output files and reports, please refer to the
 [output documentation](https://nf-co.re/nanostring/output).
 
 ## Credits
 
-nf-core/nanostring was originally written by Alexander Peltzer & Christopher Mohr. Extensive support was provided from other co-authors on the scientific or technical input required for the pipeline:
+nf-core/nanostring was originally written by Peltzer, Alexander & Mohr, Christopher. Extensive support was provided from other co-authors on the scientific or technical input required for the pipeline:
 
-- Kai Stadermann
-- Matthias Zwick
-- Germán Leparc
-- Ramona Schmid
+- Stadermann, Kai
+- Zwick, Matthias
+- Leparc, Germán
+- Schmid, Ramona
 
 ## Contributions and Support
 

assets/methods_description_template.yml

@@ -6,13 +6,17 @@ plot_type: "html"
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using nf-core/nanostring v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
+  <p>Data was processed using nf-core/nanostring v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
+  <p>${tool_citations}</p>
   <h4>References</h4>
   <ul>
-    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
-    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
+    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
+    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    ${tool_bibliography}
   </ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/nanostring" target="_blank">nf-core/nanostring</a>
+  This report has been generated by the <a href="https://github.com/nf-core/nanostring/1.2.0" target="_blank">nf-core/nanostring</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/nanostring" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/nanostring/1.2.0/output" target="_blank">documentation</a>.
 
 report_section_order:
   BD:

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+            "author_name": "nf-core/nanostring v${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [

bin/compute_gene_heatmap.R

@@ -11,31 +11,26 @@ library(tidylog)
 ###Command line argument parsing###
 args = commandArgs(trailingOnly=TRUE)
 if (length(args) < 1) {
-    stop("Usage: compute_gene_heatmap.R <annotated_counts.tsv> or compute_gene_heatmap.R <annotated_counts.tsv> <genes.yaml>", call.=FALSE)
+    stop("Usage: compute_gene_heatmap.R <annotated_counts.tsv> <sample_id_col> or compute_gene_heatmap.R <annotated_counts.tsv> <genes.yaml> <sample_id_col>", call.=FALSE)
 }
 input_counts <- args[1]
+id_col       <- tail(args, 1)
 
 #Read annotated counts
 # HEADER is always RCC_FILE + GENES + SAMPLE_ID and additional metadata such as GROUP TREATMENT OTHER_METADATA
 counts <- read.table(input_counts, sep="\t", check.names = FALSE, header=TRUE, stringsAsFactors = FALSE)
 
-if (length(args) == 2) {
+if (length(args) == 3) {
     input_genes <- args[2]
     genes <- read_yaml(input_genes)
 } else {
-    gene_cols <- counts %>% dplyr::select(- any_of(c("RCC_FILE", "SAMPLE_ID", "TIME", "TREATMENT", "OTHER_METADATA")))
+    gene_cols <- counts %>% dplyr::select(- any_of(c(unique(c("SAMPLE_ID", id_col)), "RCC_FILE", "TIME", "TREATMENT", "OTHER_METADATA")))
     genes <- colnames(gene_cols)
 }
 
 #Select counts of interest
 counts_selected <- counts %>% dplyr::select(all_of(genes))
 
-#Add proper Rownames
-rownames(counts_selected) <- counts$RCC_FILE_NAME
-
-#sort dataframe by rownames to make it easier comparable across heatmaps
-counts_selected[order(row.names(counts_selected)), ]
-
 #log2+1
 counts_selected <- log2(counts_selected + 1)
 
@@ -48,16 +43,28 @@ max_value <- max(colMax(counts_selected))
 min_value <- min(colMin(counts_selected))
 
 #Save as PDF
-
 prefix <- ""
 if (grepl("wo_HKnorm",input_counts)) {
     prefix <- "wo_HKnorm_"
 }
 
 agg_png(file = paste0(prefix, "gene_heatmap_mqc.png"), width = 1200, height = 2000, unit = "px")
 
-Heatmap(counts_selected, name = "Gene-Count Heatmap", column_title = "Gene (log2 +1)",
-        row_title_rot = 90, row_title = "SampleID",row_dend_reorder = FALSE, show_row_dend = FALSE, row_names_side = "left",
-        show_column_dend = FALSE, col = colorRamp2(c(min_value, max_value), c("#f7f7f7", "#67a9cf")))
+#Add proper row names
+counts_matrix <- as.matrix(counts_selected)
+row.names(counts_matrix) <- counts[[id_col]]
+
+Heatmap(counts_matrix,
+        name = "Gene-Count Heatmap",
+        column_title = "Gene (log2 +1)",
+        row_order = order(row.names(counts_matrix)),
+        row_title_rot = 90,
+        row_title = "SampleID",
+        row_dend_reorder = FALSE,
+        show_row_dend = FALSE,
+        row_names_side = "left",
+        show_column_dend = FALSE,
+        col = colorRamp2(c(min_value, max_value), c("#f7f7f7", "#67a9cf"))
+    )
 
 dev.off()

bin/nacho_norm.R

@@ -10,6 +10,7 @@ if (length(args) < 2) {
 }
 input_rcc_path <- args[1]
 input_samplesheet <- args[2]
+norm_method <- args[3]
 
 #Create filelist for NachoQC
 
@@ -18,7 +19,8 @@ list_of_rccs <- dir_ls(path = input_rcc_path, glob = "*.RCC")
 ####RealCode####
 nacho_data <- load_rcc(data_directory = input_rcc_path,
                     ssheet_csv = input_samplesheet,
-                    id_colname = "RCC_FILE_NAME")
+                    id_colname = "RCC_FILE_NAME",
+                    normalisation_method = norm_method)
 
 output_base <- "./"
 
@@ -45,19 +47,12 @@ now=format(Sys.time(), "%Y%m%d%H%M")
 norm_counts <- as.data.frame(get_counts(nacho_data))
 write_tsv(norm_counts, file = paste0(now, "_normalized_counts.tsv"))
 
-
 #Write out non-hk normalized counts too
 nacho_data_no_hk <- load_rcc(data_directory = input_rcc_path,
     ssheet_csv = input_samplesheet,
-    id_colname = "RCC_FILE_NAME")
-
-#Perform normalization again but without HK (so only pos + negative controls are used)
-non_hk_normed_data <- normalise(nacho_data_no_hk,
-        nacho_data_no_hk[["housekeeping_genes"]],
-        housekeeping_norm = FALSE
-)
+    id_colname = "RCC_FILE_NAME",
+    normalisation_method = norm_method,
+    housekeeping_norm = FALSE)
 
-norm_counts_without_hks <- as.data.frame(get_counts(non_hk_normed_data))
+norm_counts_without_hks <- as.data.frame(get_counts(nacho_data_no_hk))
 write_tsv(norm_counts_without_hks, file = paste0(now, "_normalized_counts_wo_HKnorm.tsv"))
-
-

conf/modules.config

@@ -40,6 +40,7 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
+        ext.args = { "${params.normalization_method}" }
     }
 
     withName: CREATE_ANNOTATED_TABLES {
@@ -56,6 +57,7 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
+        ext.args = { "${params.heatmap_id_column}" }
     }
 
     withName: COMPUTE_GENE_SCORES {
@@ -64,6 +66,7 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
+        ext.args = { "${params.gene_score_method}" }
     }
 
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {