Merge remote-tracking branch 'upstream/dev' into dev

nf-core · Dec 29, 2023 · 3662df2 · 3662df2
2 parents 12d209b + 078e5c4
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
           - "bamcsiindex"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

diff --git a/.github/workflows/release-announcments.yml → .github/workflows/release-announcements.yml b/.github/workflows/release-announcments.yml → .github/workflows/release-announcements.yml
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#95](https://github.com/nf-core/rnavar/pull/95) - Template update from nf-core/tools 2.5 -> 2.9
 - [#97](https://github.com/nf-core/rnavar/pull/97) - Template update from nf-core/tools 2.10
 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules
+- [#111](https://github.com/nf-core/rnavar/pull/111) - Template update from nf-core/tools 2.11
+- [#117](https://github.com/nf-core/rnavar/pull/117) - Template update from nf-core/tools 2.11.1
 
 ### Fixed
 
@@ -21,8 +23,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| bcftools   | 1.17        | 1.18        |
+| bedtools   | 2.31.0      | 2.31.1      |
 | fastqc     | 0.11.9      | 0.12.1      |
-| multiqc    | 1.15        | 1.17        |
+| mosdepth   | 0.3.3       | 0.3.6       |
+| multiqc    | 1.15        | 1.18        |
+| samtools   | 1.17        | 1.18        |
 
 ## [1.0.0] nfcore/rnavar - 2022/06/20
 

diff --git a/README.md b/README.md
@@ -50,11 +50,8 @@
 
 ## Usage
 
-:::note
-If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-with `-profile test` before running the workflow on actual data.
-:::
+> [!NOTE]
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -78,11 +75,9 @@ Now, you can run the pipeline using:
 nextflow run nf-core/rnavar -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv  --outdir <OUTDIR> --genome GRCh38
 ```
 
-:::warning
-Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-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).
-:::
+> [!WARNING]
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those 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 and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters).
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnavar/releases/tag/dev" target="_blank">nf-core/rnavar</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnavar/tree/dev" target="_blank">nf-core/rnavar</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/rnavar/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:

diff --git a/assets/slackreport.json b/assets/slackreport.json
@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/rnavar v${version} - ${runName}",
+            "author_name": "nf-core/rnavar ${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": [

diff --git a/conf/modules.config b/conf/modules.config
@@ -97,7 +97,7 @@ process {
 process {
 
     withName: MULTIQC {
-        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/reports"},
             mode: params.publish_dir_mode,
@@ -120,7 +120,7 @@ process {
     // ALIGN_STAR
 
     withName: STAR_ALIGN {
-        ext.args   = [
+        ext.args   = { [
             '--outSAMtype BAM SortedByCoordinate',
             '--readFilesCommand zcat',
             params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
@@ -129,7 +129,7 @@ process {
             params.star_max_memory_bamsort > 0 ? "--limitBAMsortRAM ${params.star_max_memory_bamsort}" : "",
             params.star_bins_bamsort > 0 ? "--outBAMsortingBinsN ${params.star_bins_bamsort}" : "",
             params.star_max_collapsed_junc > 0 ? "--limitOutSJcollapsed ${params.star_max_collapsed_junc}" : ""
-        ].join(' ').trim()
+            ].flatten().unique(false).join(' ').trim() }
         publishDir = [
             [
                 path: { "${params.outdir}/reports/stats/${meta.id}/STAR_log" },

diff --git a/docs/usage.md b/docs/usage.md
@@ -4,7 +4,7 @@
 
 > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
 
-## RUNNING THE PIPELINE
+## Running the pipeline
 
 The typical command for running the pipeline is as follows:
 

diff --git a/modules.json b/modules.json
@@ -7,202 +7,202 @@
                 "nf-core": {
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
                     },
                     "bcftools/pluginscatter": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
                     },
                     "bcftools/sort": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
                     },
                     "bedtools/merge": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
                         "installed_by": ["modules"]
                     },
                     "bedtools/sort": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f",
+                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/download": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
-                        "installed_by": ["vcf_annotate_ensemblvep", "modules", "vcf_annotate_ensemblvep_snpeff"]
+                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
+                        "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
                         "installed_by": ["modules"]
                     },
                     "gatk4/applybqsr": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f1b92874e0de01dd82fe1bf7c6a7409673578065",
                         "installed_by": ["modules"]
                     },
                     "gatk4/baserecalibrator": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "85561f483acc3bc6a885667ea431b3bb3fccdecb",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/combinegvcfs": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/haplotypecaller": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "eab2bd29e589bd05da2b47c9bf95ef10b9508699",
                         "installed_by": ["modules"]
                     },
                     "gatk4/indexfeaturefile": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/intervallisttools": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "bc93a4b8904472ce64c6bb50b1fb0a1659b9cf78",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/splitncigarreads": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/variantfiltration": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "mosdepth": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "e7ce60acc8a33fa17429e966364657a63016e870",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "snpeff/download": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
                         "installed_by": ["modules"]
                     },
                     "snpeff/snpeff": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
-                        "installed_by": ["vcf_annotate_ensemblvep_snpeff", "modules", "vcf_annotate_snpeff"]
+                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
+                        "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff", "vcf_annotate_snpeff"]
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules", "vcf_annotate_snpeff"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
-                        "installed_by": ["vcf_annotate_ensemblvep", "modules", "vcf_annotate_ensemblvep_snpeff"]
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "unzip": {