Merge pull request #700 from d4straub/export-more-qza

Added --save_intermediates
nf-core · Feb 6, 2024 · 2a23b1b · 2a23b1b
2 parents 2aa390c + 739ccbd
commit 2a23b1b
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Showing 9 changed files with 106 additions and 63 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#700](https://github.com/nf-core/ampliseq/pull/700) - Optional `--save_intermediates` to publish QIIME2 data objects (.qza) and visualisation objects (.qzv)
+
 ### `Changed`
 
 ### `Fixed`

diff --git a/conf/modules.config b/conf/modules.config
@@ -664,10 +664,10 @@ process {
 
     withName: 'QIIME2_INASV_BPAVG' {
         publishDir = [
-            path: { "${params.outdir}/qiime2/input" },
+            path: { "${params.outdir}/qiime2/barplot_average" },
             mode: params.publish_dir_mode,
             pattern: "*.qza",
-            enabled: false
+            enabled: params.save_intermediates
         ]
     }
 
@@ -758,25 +758,55 @@ process {
 
     withName: QIIME2_ALPHARAREFACTION {
         publishDir = [
-            path: { "${params.outdir}/qiime2" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            [
+                path: { "${params.outdir}/qiime2" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qzv') ? null : filename }
+            ],
+            [
+                path: { "${params.outdir}/qiime2/alpha-rarefaction" },
+                mode: params.publish_dir_mode,
+                pattern: "*.qzv",
+                enabled: params.save_intermediates
+            ]
         ]
     }
 
     withName: 'QIIME2_DIVERSITY_CORE|QIIME2_DIVERSITY_ALPHA|QIIME2_DIVERSITY_BETA|QIIME2_DIVERSITY_BETAORD' {
         publishDir = [
-            path: { "${params.outdir}/qiime2/diversity" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qza') ? null : filename }
+            [
+                path: { "${params.outdir}/qiime2/diversity" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qza') || filename.endsWith('.qzv') ? null : filename }
+            ],
+            [
+                path: { "${params.outdir}/qiime2/diversity/qza_qzv" },
+                mode: params.publish_dir_mode,
+                pattern: "*{.qza,.qzv}",
+                enabled: params.save_intermediates
+            ],
+            [
+                path: { "${params.outdir}/qiime2/diversity/qza_qzv" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.endsWith('.qza') ? filename : null },
+                enabled: params.save_intermediates
+            ]
         ]
     }
 
     withName: QIIME2_DIVERSITY_ADONIS {
         publishDir = [
-            path: { "${params.outdir}/qiime2/diversity/beta_diversity" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            [
+                path: { "${params.outdir}/qiime2/diversity/beta_diversity" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qzv') ? null : filename }
+            ],
+            [
+                path: { "${params.outdir}/qiime2/diversity/beta_diversity/adonis" },
+                mode: params.publish_dir_mode,
+                pattern: "*.qzv",
+                enabled: params.save_intermediates
+            ]
         ]
     }
 

diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf
@@ -11,6 +11,7 @@ process QIIME2_ALPHARAREFACTION {
 
     output:
     path("alpha-rarefaction/*"), emit: rarefaction
+    path("*.qzv")              , emit: qzv
     path "versions.yml"        , emit: versions
 
     when:

diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_ADONIS {
 
     output:
     path("adonis/*")     , emit: html
+    path("*.qzv")        , emit: qzv
     path "versions.yml"  , emit: versions
 
     when:

diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_ALPHA {
 
     output:
     path("alpha_diversity/*"), emit: alpha
+    path("*.qzv")            , emit: qzv
     path "versions.yml"      , emit: versions
 
     when:

diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_BETA {
 
     output:
     path("beta_diversity/*"), emit: beta
+    path("*.qzv")           , emit: qzv
     path "versions.yml"     , emit: versions
 
     when:

diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_BETAORD {
 
     output:
     path("beta_diversity/*"), emit: beta
+    path("*.qzv")           , emit: qzv
     path "versions.yml"     , emit: versions
 
     when:

diff --git a/nextflow.config b/nextflow.config
@@ -22,58 +22,59 @@ params {
     metadata                   = null
 
     // Other options
-    trunc_qmin        = 25
-    trunc_rmin        = 0.75
-    trunclenf         = null
-    trunclenr         = null
-    max_ee            = 2
-    max_len           = null
-    ignore_failed_filtering = false
-    min_len           = 50
-    metadata_category = null
-    metadata_category_barplot = null
-    double_primer     = false
-    retain_untrimmed  = false
-    cutadapt_min_overlap = 3
-    cutadapt_max_error_rate = 0.1
-    exclude_taxa      = "mitochondria,chloroplast"
-    min_frequency     = 1
-    min_samples       = 1
-    multiple_sequencing_runs = false
-    single_end        = false
-    sample_inference  = "independent"
-    illumina_novaseq  = false
-    illumina_pe_its   = false
-    concatenate_reads = false
-    cut_its           = "none"
-    its_partial       = 0
-    picrust           = false
-    sbdiexport        = false
-    addsh             = false
-    tax_agglom_min    = 2
-    tax_agglom_max    = 6
-    min_read_counts   = 1
-    ignore_failed_trimming = false
-    ignore_empty_input_files = false
-    qiime_adonis_formula = null
-    seed              = 100
-    filter_ssu        = null
-    min_len_asv       = null
-    max_len_asv       = null
-    filter_codons     = null
-    orf_start         = 1
-    orf_end           = null
-    stop_codons       = "TAA,TAG"
-    pplace_tree       = null
-    pplace_aln        = null
-    pplace_model      = null
-    pplace_alnmethod  = 'hmmer'
-    pplace_taxonomy   = null
-    pplace_name       = null
-    diversity_rarefaction_depth  = 500
-    ancom_sample_min_count = 1
-    vsearch_cluster   = null
-    vsearch_cluster_id= 0.97
+    save_intermediates         = false
+    trunc_qmin                 = 25
+    trunc_rmin                 = 0.75
+    trunclenf                  = null
+    trunclenr                  = null
+    max_ee                     = 2
+    max_len                    = null
+    ignore_failed_filtering    = false
+    min_len                    = 50
+    metadata_category          = null
+    metadata_category_barplot  = null
+    double_primer              = false
+    retain_untrimmed           = false
+    cutadapt_min_overlap       = 3
+    cutadapt_max_error_rate    = 0.1
+    exclude_taxa               = "mitochondria,chloroplast"
+    min_frequency              = 1
+    min_samples                = 1
+    multiple_sequencing_runs   = false
+    single_end                 = false
+    sample_inference           = "independent"
+    illumina_novaseq           = false
+    illumina_pe_its            = false
+    concatenate_reads          = false
+    cut_its                    = "none"
+    its_partial                = 0
+    picrust                    = false
+    sbdiexport                 = false
+    addsh                      = false
+    tax_agglom_min             = 2
+    tax_agglom_max             = 6
+    min_read_counts            = 1
+    ignore_failed_trimming     = false
+    ignore_empty_input_files   = false
+    qiime_adonis_formula       = null
+    seed                       = 100
+    filter_ssu                 = null
+    min_len_asv                = null
+    max_len_asv                = null
+    filter_codons              = null
+    orf_start                  = 1
+    orf_end                    = null
+    stop_codons                = "TAA,TAG"
+    pplace_tree                = null
+    pplace_aln                 = null
+    pplace_model               = null
+    pplace_alnmethod           = 'hmmer'
+    pplace_taxonomy            = null
+    pplace_name                = null
+    diversity_rarefaction_depth= 500
+    ancom_sample_min_count     = 1
+    vsearch_cluster            = null
+    vsearch_cluster_id         = 0.97
 
     // Report options
     report_template   = "${projectDir}/assets/report_template.Rmd"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -57,6 +57,11 @@
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
+                "save_intermediates": {
+                    "type": "boolean",
+                    "description": "Save intermediate results such as QIIME2's qza and qzv files",
+                    "fa_icon": "fas fa-folder-open"
+                },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",