update NORM meta in abundance_differential_filter (#7302)

* modified abundance_differential_filter to use meta_exp in deseq_norm and limma_norm, and updated test snapshots * update snapshot * update snapshot * revert order to call modules * revert test name * update snapshot * update snapshot * fix bug related to norm_inputs * avoid running multiple times NORM unecessarily by using unique(). Updated snapshots * remove view() * add back norm_inputs to avoid repeated computation of all the contrasts * distinguish contrasts_for_diff and contrasts_for_norm * remove unique() * add view to check everything is right * update view * update view * remerge criteria but with def meta at the beginning * remove view. bug fixed. --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
nf-core · Jan 16, 2025 · 2b977a4 · 2b977a4
1 parent 83ba95c
commit 2b977a4
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diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf
@@ -31,15 +31,16 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
 
     // Set up how the channels crossed below will be used to generate channels for processing
     def criteria = multiMapCriteria { meta_input, abundance, analysis_method, fc_threshold, stat_threshold, meta_exp, samplesheet, meta_contrasts, variable, reference, target ->
+        def meta_for_diff = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ]
+        def meta_input_new = meta_input + [ 'method': analysis_method ]
         samples_and_matrix:
-            meta_map = meta_input + [ 'method': analysis_method ]
-            [meta_map, samplesheet, abundance]
-        contrasts:
-            meta_map = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ]
-            [ meta_map, variable, reference, target ]
+            [ meta_input_new, samplesheet, abundance ]
+        contrasts_for_diff:
+            [ meta_for_diff, variable, reference, target ]
         filter_params:
-            meta_map = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ]
-            [meta_map, [ 'fc_threshold': fc_threshold, 'stat_threshold': stat_threshold ]]
+            [ meta_for_diff, [ 'fc_threshold': fc_threshold, 'stat_threshold': stat_threshold ]]
+        contrasts_for_norm:
+            [ meta_input_new, variable, reference, target ]
     }
 
     // For DIFFERENTIAL modules we need to cross the things we're iterating so we
@@ -70,13 +71,13 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     // LIMMA_NORM directly. It internally runs normalization + DE analysis.
 
     LIMMA_NORM(
-        norm_inputs.contrasts.filter{it[0].method == 'limma'}.first(),
+        norm_inputs.contrasts_for_norm.filter{it[0].method == 'limma'},
         norm_inputs.samples_and_matrix.filter{it[0].method == 'limma'}
     )
 
     LIMMA_DIFFERENTIAL(
-        inputs.contrasts.filter{it[0].method == 'limma'},
-        inputs.samples_and_matrix.filter { it[0].method == 'limma' }
+        inputs.contrasts_for_diff.filter{ it[0].method == 'limma' },
+        inputs.samples_and_matrix.filter{ it[0].method == 'limma' }
     )
 
     // ----------------------------------------------------
@@ -91,14 +92,14 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     // DESEQ2_NORM directly. It internally runs normalization + DE analysis.
 
     DESEQ2_NORM(
-        norm_inputs.contrasts.filter{it[0].method == 'deseq2'}.first(),
+        norm_inputs.contrasts_for_norm.filter{it[0].method == 'deseq2'},
         norm_inputs.samples_and_matrix.filter{it[0].method == 'deseq2'},
         ch_control_features.first(),
         ch_transcript_lengths.first()
     )
 
     DESEQ2_DIFFERENTIAL(
-        inputs.contrasts.filter{it[0].method == 'deseq2'},
+        inputs.contrasts_for_diff.filter{it[0].method == 'deseq2'},
         inputs.samples_and_matrix.filter{it[0].method == 'deseq2'},
         ch_control_features.first(),
         ch_transcript_lengths.first()
@@ -112,7 +113,7 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     // not produce a normalized matrix.
 
     PROPR_PROPD(
-        inputs.contrasts.filter{it[0].method == 'propd'},
+        inputs.contrasts_for_diff.filter{it[0].method == 'propd'},
         inputs.samples_and_matrix.filter { it[0].method == 'propd' }
     )
 

diff --git a/subworkflows/nf-core/abundance_differential_filter/meta.yml b/subworkflows/nf-core/abundance_differential_filter/meta.yml
@@ -133,7 +133,7 @@ output:
 authors:
   - "@pinin4fjords"
   - "@bjlang"
-  - "@araiz2001"
+  - "@caraiz2001"
   - "@suzannejin"
 maintainers:
   - "@pinin4fjords"

diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config
@@ -1,10 +1,14 @@
 process {
     withName: 'DESEQ2_DIFFERENTIAL' {
-        ext.args = { "--round_digits 5 --blocking_variables $meta.blocking --vs_method rlog" }
+        ext.args = { [
+            "--round_digits 5",
+            "--vs_method rlog",
+            (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking"
+        ].join(' ').trim() }
         ext.prefix = { "${meta.id}_${meta.method}" }
     }
 
     withName: 'DESEQ2_NORM' {
-        ext.prefix = { "${meta.id}_${meta.method}_voom_norm" }
+        ext.prefix = { "${meta.id}_${meta.method}_norm" }
     }
 }
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config
@@ -1,6 +1,10 @@
 process {
     withName: 'DESEQ2_DIFFERENTIAL' {
-        ext.args = { "--round_digits 5 --blocking_variables $meta.blocking --vs_method rlog" }
+        ext.args = { [
+            "--round_digits 5",
+            "--vs_method rlog",
+            (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking"
+        ].join(' ').trim() }
         ext.prefix = { "${meta.id}_${meta.method}" }
     }
 

diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config
@@ -1,6 +1,10 @@
 process {
     withName: 'DESEQ2_DIFFERENTIAL' {
-        ext.args = { "--round_digits 5 --blocking_variables $meta.blocking --vs_method rlog" }
+        ext.args = { [
+            "--round_digits 5",
+            "--vs_method rlog",
+            (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking"
+        ].join(' ').trim() }
         ext.prefix = { "${meta.id}_${meta.method}" }
     }
 

diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
 
     test("deseq2 - mouse - basic") {
         config './deseq2_basic.config'
-        tag "deseq2"
+        tag "deseq2_basic"
 
         when {
             workflow {
@@ -74,7 +74,7 @@ nextflow_workflow {
 
     test("limma - basic - microarray") {
         config './limma_basic_microarray.config'
-        tag "limma"
+        tag "limma_basic_microarray"
 
         setup {
             run("UNTAR") {