Massive conda update

.github/workflows/ci.yml

@@ -12,12 +12,15 @@ on:
       - dev
 
 env:
-  NFTEST_VER: "0.9.0"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+  NFT_VER: "0.9.0"
+  NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
-  TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"
-  SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+  TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"
 
 # Cancel if a newer run is started
 concurrency:
@@ -238,13 +241,16 @@ jobs:
           - tags: "cnvkit/antitarget"
           - tags: "cnvkit/batch"
           - tags: "cnvkit/reference"
-          - tags: "deepvariant"
+          - tags: "controlfreec/assesssignificance"
+          - tags: "controlfreec/freec"
+          - tags: "deepvariant/rundeepvariant"
           - tags: "dragmap/align"
           - tags: "dragmap/hashtable"
           - tags: "ensemblvep/download"
           - tags: "ensemblvep/vep"
           - tags: "fastp"
           - tags: "fastqc"
+          - tags: "fgbio/callmolecularconsensusreads"
           - tags: "fgbio/fastqtobam"
           - tags: "freebayes"
           - tags: "gatk4/applybqsr"
@@ -266,18 +272,17 @@ jobs:
           - tags: "samtools/convert"
           - tags: "samtools/mpileup"
           - tags: "samtools/stats"
+          - tags: "sentieon/bwamem"
+          - tags: "sentieon/haplotyper"
           - tags: "snpeff/snpeff"
+          - tags: "spring/decompress"
           - tags: "strelka/germline"
           - tags: "strelka/somatic"
           - tags: "subworkflows/utils_nfvalidation_plugin"
           - tags: "tabix/bgziptabix"
           - tags: "tabix/tabix"
           - tags: "tiddit/sv"
           - tags: "untar"
-          - tags: "pipeline_sarek"
-        include:
-          - tags: "pipeline_sarek"
-            profile: "test,docker"
 
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
@@ -295,7 +300,7 @@ jobs:
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
         with:
-          version: ${{ env.NFTEST_VER }}
+          version: ${{ env.NFT_VER }}
 
       - name: Setup apptainer
         if: matrix.profile == 'singularity'
@@ -339,13 +344,15 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 
-      # Test the module
+      # Test the component
       - name: Run nf-test
         run: |
           nf-test test \
-            --profile=${{ matrix.profile }} \
+            --profile="+${{ matrix.profile }}" \
             --tag ${{ matrix.tags }} \
             --tap=test.tap \
+            --junitxml=test.xml \
+            --debug \
             --verbose
 
   confirm-pass:

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev
 - [1653](https://github.com/nf-core/sarek/pull/1653) - Updates `sarek_subway` files with `lofreq`
 - [1660](https://github.com/nf-core/sarek/pull/1642) - Add `--length_required` for minimal reads length with `FASTP`
+- [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update
 
 ### Changed
 
@@ -29,12 +30,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Dependencies
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| `lofreq`   |             | 2.1.5       |
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| `deepvariant` | 1.5.0       | 1.6.1       |
+| `ensemblvep`  | 111.0       | 112.0       |
+| `fgbio`       | 2.0.2       | 2.1.2       |
+| `htslib`      | 1.20        | 1.21        |
+| `lofreq`      |             | 2.1.5       |
+| `multiqc`     | 1.21        | 1.25.1      |
+| `samtools`    | 1.20        | 1.21        |
 
 ### Parameters
 
+| Params          | Status  |
+| --------------- | ------- |
+| `snpeff_db`     | Updated |
+| `snpeff_genome` | Removed |
+
 ## [3.4.4](https://github.com/nf-core/sarek/releases/tag/3.4.4) - Ruopsokjåkhå
 
 Ruopsokjåkhå is another peak of the Pårte massif.

conf/modules/annotate.config

@@ -64,12 +64,12 @@ process {
     // BCFTOOLS ANNOTATE
     if (params.tools && params.tools.split(',').contains('bcfann')) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
-            ext.args   = { '--output-type z' }
+            ext.args   = { '--output-type z --write-index=tbi' }
             ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' }
             publishDir = [
                     mode: params.publish_dir_mode,
                     path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
-                    pattern: "*{gz}"
+                    pattern: "*{gz,gz.tbi}"
                 ]
         }
     }

conf/modules/deepvariant.config

@@ -15,8 +15,8 @@
 
 process {
 
-    withName: 'DEEPVARIANT' {
-        ext.args   = { params.wes ?  "--model_type WES" : "--model_type WGS" }
+    withName: 'DEEPVARIANT_RUNDEEPVARIANT' {
+        ext.args   = { params.wes ?  "--model_type=WES" : "--model_type=WGS" }
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.baseName}" }
         ext.when   = { params.tools && params.tools.split(',').contains('deepvariant') }
         publishDir = [

conf/modules/umi.config

@@ -73,7 +73,7 @@ process {
     }
 
     withName: 'CALLUMICONSENSUS' {
-        ext.args   = { '-M 1 -S Coordinate' }
+        ext.args   = { '-S Coordinate' }
         ext.prefix = { "${meta.id}_umi-consensus" }
         publishDir = [
             path: { "${params.outdir}/preprocessing/umi/${meta.sample}" },

conf/test/tools_germline_deepvariant.config

@@ -0,0 +1,23 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity> --outdir <OUTDIR>
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    input                  = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
+    genome                 = null
+    igenomes_ignore        = true
+    fasta                  = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta"
+    fasta_fai              = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta.fai"
+    intervals              = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.bed"
+    nucleotides_per_second = 20
+    step                   = 'variant_calling'
+    tools                  = null
+    wes                    = true
+}