Merge pull request #436 from genomic-medicine-sweden/skip_qualimap

add skip_qualimap and skip_eklipse parameters
nf-core · Oct 18, 2023 · 16d6831 · 16d6831
2 parents ae33272 + 9b1b6c6
commit 16d6831
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Showing 9 changed files with 49 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - A new parameter to skip filtering based on vep results [#416](https://github.com/nf-core/raredisease/pull/416)
 - A `metromap` representating the core parts of the pipeline [#428](https://github.com/nf-core/raredisease/pull/428)
 - Metromap and logos for light and dark theme [#432](https://github.com/nf-core/raredisease/pull/432)
+- New parameters to skip qualimap and eklipse (`--skip_qualimap` and `--skip_eklipse`) [#436](https://github.com/nf-core/raredisease/pull/436)
 
 ### `Changed`
 

diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config
@@ -26,12 +26,14 @@ process {
         ]
     }
 
-    withName: '.*CALL_SV_MT:EKLIPSE' {
-        publishDir = [
-            path: { "${params.outdir}/call_sv/mitochondria" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+    if (!params.skip_eklipse){
+        withName: '.*CALL_SV_MT:EKLIPSE' {
+            publishDir = [
+                path: { "${params.outdir}/call_sv/mitochondria" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
     }
 }
 
diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config
@@ -33,8 +33,10 @@ process {
         ext.prefix = { "${meta.id}_hsmetrics" }
     }
 
-    withName: '.*QC_BAM:QUALIMAP_BAMQC' {
-        ext.prefix = { "${meta.id}_qualimap" }
+    if (!params.skip_qualimap) {
+        withName: '.*QC_BAM:QUALIMAP_BAMQC' {
+            ext.prefix = { "${meta.id}_qualimap" }
+        }
     }
 
     withName: '.*QC_BAM:TIDDIT_COV' {

diff --git a/conf/test.config b/conf/test.config
@@ -25,6 +25,8 @@ params {
 
     // analysis params
     skip_cnv_calling   = true
+    skip_eklipse       = true
+    skip_qualimap      = true
     skip_mt_annotation = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
 
     // Input data

diff --git a/conf/test_one_sample.config b/conf/test_one_sample.config
@@ -25,6 +25,8 @@ params {
 
     // analysis params
     skip_cnv_calling = true
+    skip_eklipse       = true
+    skip_qualimap      = true
     skip_mt_annotation = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
 
     // Input data

diff --git a/nextflow.config b/nextflow.config
@@ -25,6 +25,8 @@ params {
     bait_padding               = 100
     save_mapped_as_cram        = false
     skip_cnv_calling           = false
+    skip_eklipse               = false
+    skip_qualimap              = false
     skip_snv_annotation        = false
     skip_sv_annotation         = false
     skip_mt_annotation         = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -388,6 +388,16 @@
                     "description": "Specifies whether or not to skip CNV calling.",
                     "fa_icon": "fas fa-toggle-on"
                 },
+                "skip_eklipse": {
+                    "type": "boolean",
+                    "description": "Specifies whether or not to skip eKLIPse.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
+                "skip_qualimap": {
+                    "type": "boolean",
+                    "description": "Specifies whether or not to skip Qualimap.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "skip_mt_annotation": {
                     "type": "boolean",
                     "description": "Specifies whether or not to skip annotation of mitochondrial variants.",

diff --git a/subworkflows/local/qc_bam.nf b/subworkflows/local/qc_bam.nf
@@ -29,6 +29,7 @@ workflow QC_BAM {
 
     main:
         ch_versions = Channel.empty()
+        ch_qualimap = Channel.empty()
 
         PICARD_COLLECTMULTIPLEMETRICS (ch_bam_bai, ch_genome_fasta, ch_genome_fai)
 
@@ -39,7 +40,10 @@ workflow QC_BAM {
 
         PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]])
 
-        QUALIMAP_BAMQC (ch_bam, [])
+        if (!params.skip_qualimap) {
+            ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results
+            ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first())
+        }
 
         TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input
 
@@ -60,7 +64,6 @@ workflow QC_BAM {
 
         ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
-        ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first())
         ch_versions = ch_versions.mix(TIDDIT_COV.out.versions.first())
         ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions.first())
         ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first())
@@ -70,7 +73,7 @@ workflow QC_BAM {
     emit:
         multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ]
         hs_metrics       = PICARD_COLLECTHSMETRICS.out.metrics       // channel: [ val(meta), path(metrics) ]
-        qualimap_results = QUALIMAP_BAMQC.out.results                // channel: [ val(meta), path(qualimap_dir) ]
+        qualimap_results = ch_qualimap                               // channel: [ val(meta), path(qualimap_dir) ]
         tiddit_wig       = TIDDIT_COV.out.wig                        // channel: [ val(meta), path(wig) ]
         bigwig           = UCSC_WIGTOBIGWIG.out.bw                   // channel: [ val(meta), path(bw) ]
         d4               = MOSDEPTH.out.per_base_d4                  // channel: [ val(meta), path(d4) ]

diff --git a/subworkflows/local/variant_calling/call_sv_MT.nf b/subworkflows/local/variant_calling/call_sv_MT.nf
@@ -11,19 +11,27 @@ workflow CALL_SV_MT {
         ch_fasta        // channel: [mandatory] [ val(meta), path(fasta) ]
 
     main:
-        ch_versions = Channel.empty()
+        ch_versions       = Channel.empty()
+        ch_eklipse_del    = Channel.empty()
+        ch_eklipse_genes  = Channel.empty()
+        ch_eklipse_circos = Channel.empty()
 
-        EKLIPSE(ch_bam_bai,[])
+        if (!params.skip_eklipse){
+            EKLIPSE(ch_bam_bai,[])
+            ch_eklipse_del    = EKLIPSE.out.deletions
+            ch_eklipse_genes  = EKLIPSE.out.genes
+            ch_eklipse_circos = EKLIPSE.out.circos
+            ch_versions = ch_versions.mix(EKLIPSE.out.versions.first())
+       }
 
         MT_DELETION(ch_bam_bai, ch_fasta)
 
-        ch_versions = ch_versions.mix(EKLIPSE.out.versions.first())
         ch_versions = ch_versions.mix(MT_DELETION.out.versions.first())
 
     emit:
-        eklipse_del    = EKLIPSE.out.deletions         // channel: [ val(meta), path(csv) ]
-        eklipse_genes  = EKLIPSE.out.genes             // channel: [ val(meta), path(csv) ]
-        eklipse_circos = EKLIPSE.out.circos            // channel: [ val(meta), path(png) ]
+        eklipse_del    = ch_eklipse_del                // channel: [ val(meta), path(csv) ]
+        eklipse_genes  = ch_eklipse_genes              // channel: [ val(meta), path(csv) ]
+        eklipse_circos = ch_eklipse_circos             // channel: [ val(meta), path(png) ]
         mt_del_result  = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ]
         versions       = ch_versions                   // channel: [ path(versions.yml) ]
 }