Merge pull request #78 from alessiovignoli/zip

Zip
nf-core · Oct 20, 2023 · 868d3ef · 868d3ef
2 parents f17a59f + d9773a3
commit 868d3ef
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Showing 8 changed files with 138 additions and 12 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 [#60](https://github.com/nf-core/multiplesequencealign/issues/60) - Add module Tcoffee3D_align and handle structures input
 [#35](https://github.com/nf-core/multiplesequencealign/issues/35) - Add module MUSCLE5_SUPER5
 [#59](https://github.com/nf-core/multiplesequencealign/issues/59) - Add support for passing structure template in samplesheet.
+[#77](https://github.com/nf-core/multiplesequencealign/issues/77) - Add module zip
 
 ### `Fixed`
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -41,21 +41,25 @@ process {
     withName: ".*ALIGN"{
         ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.argsaligner_clean}" }
         ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
-        publishDir = [
-            path: { "${params.outdir}/alignment/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        if ( params.skip_compress ) {
+            publishDir = [
+                path: { "${params.outdir}/alignment/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
     }
 
     withName: "MAFFT|CLUSTALO_ALIGN|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN|MUSCLE5_SUPER5"{
         ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.argsaligner_clean}" }
         ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
-        publishDir = [
-            path: { "${params.outdir}/alignment/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        if ( params.skip_compress ) {
+            publishDir = [
+                path: { "${params.outdir}/alignment/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
     }
 
     withName: ".*EVAL"{
@@ -73,6 +77,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
     withName: "TCOFFEE_SEQREFORMAT_SIM|CALCULATE_SEQSTATS"{
         publishDir = [
             path: { "${params.outdir}/stats/${task.process.tokenize(':')[-1].toLowerCase()}" },
@@ -88,9 +93,11 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
     withName: "FASTQC"{
         ext.args = '--quiet'
     }
+
     withName: "CUSTOM_DUMPSOFTWAREVERSIONS"{
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
@@ -108,6 +115,13 @@ process {
         ]
     }
 
-
+    withName: 'ZIP' {
+        ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.argsaligner_clean}" }
+        publishDir = [
+            path: { "${params.outdir}/alignment/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
 }
diff --git a/modules.json b/modules.json
@@ -69,6 +69,11 @@
                         "branch": "master",
                         "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
                         "installed_by": ["modules"]
+                    },
+                    "zip": {
+                        "branch": "master",
+                        "git_sha": "9ba4f5972ae27474f752ddb20e855f48047aa6c8",
+                        "installed_by": ["modules"]
                     }
                 }
             }

diff --git a/modules/nf-core/zip/main.nf b/modules/nf-core/zip/main.nf
diff --git a/modules/nf-core/zip/meta.yml b/modules/nf-core/zip/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -19,7 +19,8 @@ params {
 
     // Stats
     skip_stats                 = false
-    skip_eval                  = false 
+    skip_eval                  = false
+    skip_compress               = false
 
     // MultiQC options
     multiqc_config             = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -80,6 +80,18 @@
                 }
             }
         },
+        "compression": {
+            "title": "Compression",
+            "type": "object",
+            "description": "Define wether to run compression",
+            "default": "",
+            "properties": {
+                "skip_compress": {
+                    "type": "boolean",
+                    "description": "Skip the compression of all alignment files"
+                }
+            }
+        },
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -285,6 +297,9 @@
         {
             "$ref": "#/definitions/eval_options"
         },
+        {
+            "$ref": "#/definitions/compression"
+        },
         {
             "$ref": "#/definitions/institutional_config_options"
         },

diff --git a/workflows/multiplesequencealign.nf b/workflows/multiplesequencealign.nf
@@ -46,10 +46,12 @@ include { CREATE_TCOFFEETEMPLATE      } from '../modules/local/create_tcoffee_te
 //
 // MODULE: Installed directly from nf-core/modules
 //
+
 include { FASTQC                      } from '../modules/nf-core/fastqc/main'
 include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 include { UNTAR                       } from '../modules/nf-core/untar/main'
+include { ZIP                         } from '../modules/nf-core/zip/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -153,6 +155,7 @@ workflow MULTIPLESEQUENCEALIGN {
     ALIGN(ch_seqs, ch_tools, ch_structures_template )
     ch_versions = ch_versions.mix(ALIGN.out.versions)
 
+
     //
     // Evaluate the quality of the alignment
     //
@@ -166,6 +169,14 @@ workflow MULTIPLESEQUENCEALIGN {
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 
+    //
+    // MODULE: zip
+    //
+    if( !params.skip_compress ){
+        ZIP(ALIGN.out.msa)
+        ch_versions = ch_versions.mix(ZIP.out.versions)
+    }
+
     //
     // MODULE: MultiQC
     //