Merge branch 'dev' into upd_fix

nf-core · Oct 30, 2024 · 86f0373 · 86f0373
2 parents 4606957 + 31249da
commit 86f0373
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Showing 28 changed files with 92 additions and 90 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638)
+- Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
 - Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
 - Update output file name prefix for upd and chromograph to sample-based [#620](https://github.com/nf-core/raredisease/pull/620)
 - Update tools [#619](https://github.com/nf-core/raredisease/pull/619)
@@ -28,17 +30,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Tool updates
 
-| Tool     | Old version | New version |
-| -------- | ----------- | ----------- |
-| bcftools | 1.18        | 1.20        |
-| genmod   | 3.8.2       | 3.8.3       |
-| mosdepth | 0.3.6       | 0.3.8       |
-| multiqc  | 1.21        | 1.25.1      |
-| picard   | 3.1.1       | 3.2.0       |
-| samtools | 1.19.2      | 1.21        |
-| sentieon | 202308.02   | 202308.03   |
-| stranger | 0.8.1       | 0.9.1       |
-| tabix    | 1.19.1      | 1.20        |
+| Tool       | Old version | New version |
+| ---------- | ----------- | ----------- |
+| bcftools   | 1.18        | 1.20        |
+| ensemblvep | 112         | 113         |
+| genmod     | 3.8.2       | 3.8.3       |
+| mosdepth   | 0.3.6       | 0.3.8       |
+| multiqc    | 1.21        | 1.25.1      |
+| picard     | 3.1.1       | 3.2.0       |
+| samtools   | 1.19.2      | 1.21        |
+| sentieon   | 202308.02   | 202308.03   |
+| stranger   | 0.8.1       | 0.9.1       |
+| tabix      | 1.19.1      | 1.20        |
 
 ## 2.2.0 - Dogmatix [2024-09-13]
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -18,6 +18,7 @@ export_plots: true
 
 run_modules:
   - fastqc
+  - fastp
   - qualimap
   - picard
   - mosdepth
@@ -33,6 +34,8 @@ module_order:
       name: "Picard"
   - qualimap:
       name: "Qualimap"
+  - fastp:
+      name: "fastp"
   - mosdepth:
       name: "Mosdepth"
   - peddy:
@@ -41,6 +44,6 @@ module_order:
 extra_fn_clean_exts:
   - "_sorted_md"
   - type: regex
-    pattern: "_T[0-9]"
+    pattern: "_LNUMBER[0-9]{1,}"
 
 disable_version_detection: true
diff --git a/conf/modules/annotate_mobile_elements.config b/conf/modules/annotate_mobile_elements.config
@@ -37,7 +37,7 @@ process {
             '--appris --biotype --buffer_size 100 --canonical --cache --ccds',
             '--compress_output bgzip --distance 5000 --domains',
             '--exclude_predicted --force_overwrite --format vcf',
-            '--fork 4 --hgvs --humdiv --max_sv_size 248956422 --merged',
+            '--hgvs --humdiv --max_sv_size 248956422 --merged',
             '--no_progress --numbers --per_gene --polyphen p',
             '--protein --offline --regulatory --sift p',
             '--symbol --tsl --uniprot --vcf'

diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config
@@ -29,7 +29,7 @@ process {
             '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz',
             '--distance 0',
             '--buffer_size 20000',
-            '--format vcf --fork 4 --max_sv_size 248956422',
+            '--format vcf --max_sv_size 248956422',
             '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
             '--domains --exclude_predicted --force_overwrite',
             '--hgvs --humdiv --no_progress --numbers',

diff --git a/conf/modules/annotate_structural_variants.config b/conf/modules/annotate_structural_variants.config
@@ -37,13 +37,13 @@ process {
 
     withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV' {
         ext.args = { [
-            '--dir_cache vep_cache',
-            '--dir_plugins vep_cache/Plugins',
+            '--dir_cache cache',
+            '--dir_plugins cache/Plugins',
             '--plugin pLI,pLI_values.txt',
             '--appris --biotype --buffer_size 100 --canonical --cache --ccds',
             '--compress_output bgzip --distance 5000 --domains',
             '--exclude_predicted --force_overwrite --format vcf',
-            '--fork 4 --hgvs --humdiv --max_sv_size 248956422 --merged',
+            '--hgvs --humdiv --max_sv_size 248956422 --merged',
             '--no_progress --numbers --per_gene --polyphen p',
             '--protein --offline --regulatory --sift p',
             '--symbol --tsl --uniprot --vcf'

diff --git a/conf/modules/call_sv_germlinecnvcaller.config b/conf/modules/call_sv_germlinecnvcaller.config
@@ -34,4 +34,9 @@ process {
         ext.prefix = { "${meta.id}_gatkcnv_segments_refiltered" }
         ext.args = { '--output-type z --exclude "N_ALT = 0" ' }
     }
+
+    withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:SVDB_MERGE_GCNVCALLER' {
+        ext.args   = '--notag --pass_only'
+        ext.prefix = { "${meta.id}_gcnvcaller" }
+    }
 }
diff --git a/conf/wes.config b/conf/wes.config
diff --git a/modules.json b/modules.json
@@ -123,12 +123,12 @@
                     },
                     "ensemblvep/filtervep": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                         "installed_by": ["modules"]
                     },
                     "expansionhunter": {

diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml
diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
diff --git a/nextflow.config b/nextflow.config
@@ -283,11 +283,6 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Load wes.config if --analysis_type='wes'
-if (params.analysis_type == 'wes') {
-    includeConfig 'conf/wes.config'
-}
-
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 

diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf
@@ -30,7 +30,7 @@ workflow CALL_SNV {
         ch_dbsnp              // channel: [optional] [ val(meta), path(vcf) ]
         ch_dbsnp_tbi          // channel: [optional] [ val(meta), path(tbi) ]
         ch_call_interval      // channel: [mandatory] [ path(intervals) ]
-        ch_bait_intervals     // channel: [mandatory] [ path(intervals) ]
+        ch_target_bed         // channel: [mandatory] [ val(meta), path(bed), path(index) ]
         ch_ml_model           // channel: [mandatory] [ path(model) ]
         ch_par_bed            // channel: [optional] [ val(meta), path(bed) ]
         ch_case_info          // channel: [mandatory] [ val(case_info) ]
@@ -55,7 +55,7 @@ workflow CALL_SNV {
                 ch_genome_bam_bai,
                 ch_genome_fasta,
                 ch_genome_fai,
-                ch_bait_intervals,
+                ch_target_bed,
                 ch_par_bed,
                 ch_case_info,
                 ch_foundin_header,