Merge pull request nf-core#412 from genomic-medicine-sweden/modules_u…

…pdate Update modules to their latest nf-core version
genomic-medicine-sweden · Aug 21, 2023 · 7aa5b47 · 7aa5b47
2 parents 032fb7c + a2dfa81
commit 7aa5b47
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Showing 29 changed files with 350 additions and 287 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Sort ranked SV vcf before indexing with tabix [#393](https://github.com/nf-core/raredisease/pull/393)
 - Make target bed file optional for WGS mode (Issue [#375](https://github.com/nf-core/raredisease/issues/375)) [#395](https://github.com/nf-core/raredisease/pull/395)
 - Added constraints to block the pipeline from running CollectWgsMetrics on WES samples [#396](https://github.com/nf-core/raredisease/pull/396)
+- Updated modules from nf-core [#412](https://github.com/nf-core/raredisease/pull/412)
+
+### `Updated`
+
+| Tool         | Old version | New version |
+| ------------ | ----------- | ----------- |
+| `filter_vep` | 107         | 110         |
+| `multiqc`    | 1.14        | 1.15        |
+| `untar`      | (grep 3.4)  | (grep 3.11) |
 
 ## v1.1.1 - Abu (Patch) [2023-07-26]
 

diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config
@@ -103,8 +103,9 @@ process {
 //
 
 process {
-    withName: '.*FILTER_VEP_SNV' {
+    withName: '.*FILTERVEP_SNV' {
         ext.prefix = { "${meta.id}_clinical_snv" }
+        ext.args   = { "--filter \"HGNC_ID in ${feature_file}\"" }
     }
 
     withName: '.*BGZIPTABIX_SNV' {
@@ -118,8 +119,9 @@ process {
 }
 
 process {
-    withName: '.*FILTER_VEP_SV' {
+    withName: '.*FILTERVEP_SV' {
         ext.prefix = { "${meta.id}_clinical_sv" }
+        ext.args   = { "--filter \"HGNC_ID in ${feature_file}\"" }
     }
 
     withName: '.*BGZIPTABIX_SV' {

diff --git a/conf/test.config b/conf/test.config
@@ -52,8 +52,7 @@ params {
 }
 
 process {
-    withLabel: 'sentieon' {
-        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
-        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
+    withName: '.*FILTERVEP.*' {
+        container  = "docker.io/ensemblorg/ensembl-vep:release_107.0"
     }
 }
diff --git a/conf/test_one_sample.config b/conf/test_one_sample.config
@@ -50,3 +50,9 @@ params {
     vep_filters          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
     vep_cache_version    = 107
 }
+
+process {
+    withName: '.*FILTERVEP.*' {
+        container  = "docker.io/ensemblorg/ensembl-vep:release_107.0"
+    }
+}
diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config
@@ -0,0 +1,63 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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/raredisease -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus       = 2
+    max_memory     = '6.GB'
+    max_time       = '2.h'
+
+    // reference params
+    igenomes_ignore = true
+    mito_name       = 'MT'
+
+    // analysis params
+    skip_cnv_calling = true
+
+    // Input data
+    input          = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv'
+
+    // Genome references
+    fasta                = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta"
+    genome               = 'GRCh37'
+    gnomad_af            = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz"
+    intervals_wgs        = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list"
+    intervals_y          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
+    known_dbsnp          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
+    ml_model             = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
+    reduced_penetrance   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
+    score_config_snv     = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
+    score_config_sv      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini"
+    svdb_query_dbs       = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv"
+    target_bed           = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed"
+    variant_catalog      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json"
+    vcfanno_lua          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua"
+    vcfanno_resources    = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt"
+    vcfanno_toml         = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml"
+    vep_cache            = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz"
+    vep_filters          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
+    vep_cache_version    = 107
+}
+
+process {
+    withLabel: 'sentieon' {
+        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
+        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
+    }
+
+    withName: '.*FILTERVEP.*' {
+        container  = "docker.io/ensemblorg/ensembl-vep:release_107.0"
+    }
+}
diff --git a/modules.json b/modules.json
@@ -82,19 +82,24 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "deepvariant": {
                         "branch": "master",
-                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
+                        "git_sha": "ed67f2fadd6d2a155b296f728e6b1f8c92ddc1a6",
                         "installed_by": ["modules"]
                     },
                     "eklipse": {
                         "branch": "master",
                         "git_sha": "39656f68219340420f03bd54a68e111c86e107e6",
                         "installed_by": ["modules"]
                     },
+                    "ensemblvep/filtervep": {
+                        "branch": "master",
+                        "git_sha": "29984d70aea47d06f0062a1785d76c357dd40ea9",
+                        "installed_by": ["modules"]
+                    },
                     "expansionhunter": {
                         "branch": "master",
                         "git_sha": "0260e5d22372eae434816d6970dedf3f5adc0053",
@@ -120,9 +125,14 @@
                         "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/denoisereadcounts": {
+                        "branch": "master",
+                        "git_sha": "38c559b2a8b9a8cda62fa215521f581eb979c773",
+                        "installed_by": ["modules"]
+                    },
                     "gatk4/determinegermlinecontigploidy": {
                         "branch": "master",
-                        "git_sha": "c6257c167fb88d18f3c2797e1af331d28f7b8ae7",
+                        "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtermutectcalls": {
@@ -132,7 +142,7 @@
                     },
                     "gatk4/germlinecnvcaller": {
                         "branch": "master",
-                        "git_sha": "f6b848c6e1af9a9ecf4975aa8c8edad05e75e784",
+                        "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf",
                         "installed_by": ["modules"]
                     },
                     "gatk4/intervallisttools": {
@@ -157,7 +167,7 @@
                     },
                     "gatk4/postprocessgermlinecnvcalls": {
                         "branch": "master",
-                        "git_sha": "c6257c167fb88d18f3c2797e1af331d28f7b8ae7",
+                        "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf",
                         "installed_by": ["modules"]
                     },
                     "gatk4/preprocessintervals": {
@@ -247,12 +257,12 @@
                     },
                     "mosdepth": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "peddy": {
@@ -347,7 +357,7 @@
                     },
                     "sentieon/bwamem": {
                         "branch": "master",
-                        "git_sha": "b9172e8c26a3db5009f7872654c44587e254f094",
+                        "git_sha": "149b4746c6e16ef84f64db5bb245d5b9495fdc3f",
                         "installed_by": ["modules"]
                     },
                     "sentieon/datametrics": {
@@ -432,7 +442,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
                         "installed_by": ["modules"]
                     },
                     "upd": {

diff --git a/modules/local/filter_vep.nf b/modules/local/filter_vep.nf
diff --git a/modules/local/gatk4/collectreadcounts/main.nf b/modules/local/gatk4/collectreadcounts/main.nf
diff --git a/modules/local/gatk4/collectreadcounts/meta.yml b/modules/local/gatk4/collectreadcounts/meta.yml