Merge pull request #471 from nf-core/run-qualimap-param

`run_qualimap` param and skip qualimap/bamqc by default
nf-core · Nov 28, 2024 · 568bd06 · 568bd06
2 parents 6ea0f13 + 5666f29
commit 568bd06
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Showing 24 changed files with 968 additions and 3,596 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,10 +10,11 @@
 ### Pipeline Updates
 
 - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457)
-- 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/)
+- 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/468)
 - 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows [#467](https://github.com/nf-core/methylseq/pull/)
 - 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/469)
 - 🔧 `run_preseq` param + skip preseq/lcextrap module by default [#458](https://github.com/nf-core/methylseq/pull/470)
+- 🔧 `run_qualimap` param + skip qualimap module by default [#367](https://github.com/nf-core/methylseq/pull/471)
 
 ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
 

diff --git a/conf/modules/qualimap_bamqc.config b/conf/modules/qualimap_bamqc.config
@@ -4,5 +4,13 @@ process {
             params.genome.toString().startsWith('GRCh') ? '-gd HUMAN' : '',
             params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : ''
         ].join(" ").trim()
+        publishDir = [
+            [
+                path: { "${params.outdir}/${params.aligner}/qualimap/bamqc/" },
+                mode: params.publish_dir_mode,
+                pattern: "*",
+                enabled: params.run_qualimap
+            ]
+        ]
     }
 }
diff --git a/nextflow.config b/nextflow.config
@@ -10,85 +10,86 @@
 params {
 
     // Input options
-    input                      = null
+    input                       = null
 
     // References
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    igenomes_ignore            = false
+    genome                      = null
+    igenomes_base               = 's3://ngi-igenomes/igenomes/'
+    igenomes_ignore             = false
 
     // MultiQC options
-    multiqc_config              = null
-    multiqc_title               = null
-    multiqc_logo                = null
-    max_multiqc_email_size      = '25.MB'
-    multiqc_methods_description = null
+    multiqc_config               = null
+    multiqc_title                = null
+    multiqc_logo                 = null
+    max_multiqc_email_size       = '25.MB'
+    multiqc_methods_description  = null
 
     // Intermediate files
-    save_reference             = false
-    save_align_intermeds       = false
-    unmapped                   = false
-    save_trimmed               = false
+    save_reference               = false
+    save_align_intermeds         = false
+    unmapped                     = false
+    save_trimmed                 = false
 
     // Alignment options
-    aligner                    = 'bismark'
-    comprehensive              = false
-
-    // Qualimap options
-    bamqc_regions_file         = null
+    aligner                      = 'bismark'
+    comprehensive                = false
 
     // Library presets
-    pbat                       = false
-    rrbs                       = false
-    slamseq                    = false
-    em_seq                     = false
-    single_cell                = false
-    accel                      = false
-    cegx                       = false
-    epignome                   = false
-    zymo                       = false
+    pbat                         = false
+    rrbs                         = false
+    slamseq                      = false
+    em_seq                       = false
+    single_cell                  = false
+    accel                        = false
+    cegx                         = false
+    epignome                     = false
+    zymo                         = false
 
     // Trimming options
-    clip_r1                    = 0
-    clip_r2                    = 0
-    three_prime_clip_r1        = 0
-    three_prime_clip_r2        = 0
-    nextseq_trim               = 0
-    length_trim                = null
+    clip_r1                      = 0
+    clip_r2                      = 0
+    three_prime_clip_r1          = 0
+    three_prime_clip_r2          = 0
+    nextseq_trim                 = 0
+    length_trim                  = null
 
     // Bismark options
-    non_directional            = false
-    cytosine_report            = false
-    relax_mismatches           = false
-    num_mismatches             = 0.6
+    non_directional              = false
+    cytosine_report              = false
+    relax_mismatches             = false
+    num_mismatches               = 0.6
     // 0.6 will allow a penalty of bp * -0.6
     // For 100bp reads, this is -60. Mismatches cost -6, gap opening -5 and gap extension -2
     // So -60 would allow 10 mismatches or ~ 8 x 1-2bp indels
     // Bismark default is 0.2 (L,0,-0.2), Bowtie2 default is 0.6 (L,0,-0.6)
-    meth_cutoff                = null
-    no_overlap                 = true
-    ignore_r1                  = 0
-    ignore_r2                  = 2
-    ignore_3prime_r1           = 0
-    ignore_3prime_r2           = 2
-    known_splices              = null
-    local_alignment            = false
-    minins                     = null
-    maxins                     = null
-    nomeseq                    = false
+    meth_cutoff                  = null
+    no_overlap                   = true
+    ignore_r1                    = 0
+    ignore_r2                    = 2
+    ignore_3prime_r1             = 0
+    ignore_3prime_r2             = 2
+    known_splices                = null
+    local_alignment              = false
+    minins                       = null
+    maxins                       = null
+    nomeseq                      = false
 
     // bwa-meth options
-    min_depth                  = 0
-    ignore_flags               = false
-    methyl_kit                 = false
+    min_depth                    = 0
+    ignore_flags                 = false
+    methyl_kit                   = false
 
     // Skipping options
-    skip_trimming              = false
-    skip_deduplication         = false
-    skip_multiqc               = false
+    skip_trimming                = false
+    skip_deduplication           = false
+    skip_multiqc                 = false
 
     // Run options
-    run_preseq                 = false
+    run_preseq                   = false
+    run_qualimap                 = false
+
+    // Qualimap options
+    bamqc_regions_file           = null
 
     // Boilerplate options
     outdir                       = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -452,6 +452,11 @@
                     "type": "boolean",
                     "description": "Run preseq/lcextrap tool",
                     "fa_icon": "fas fa-fast-forward"
+                },
+                "run_qualimap": {
+                    "type": "boolean",
+                    "description": "Run qualimap/bamqc tool",
+                    "fa_icon": "fas fa-fast-forward"
                 }
             },
             "fa_icon": "fas fa-fast-forward"