Reply reviewer's comment for 2.0.0

CHANGELOG.md

@@ -76,6 +76,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [[#743]](https://github.com/nf-core/differentialabundance/pull/743) - Update `variancepartition/dream` to disable implicit parallelism ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst)).
 - [[#743]](https://github.com/nf-core/differentialabundance/pull/743) - Update `variancepartition/dream` to disable implicit parallelism ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila), [@apeltzer](https://github.com/apeltzer), and [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#734](https://github.com/nf-core/differentialabundance/pull/734)] - Update `variancepartition/dream` module and `abundance_differential_filter` subworkflow ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila) and [@apeltzer](https://github.com/apeltzer)).
 - [[#732](https://github.com/nf-core/differentialabundance/pull/732)] - Bump `nf-metro` pin to `>=0.7.2` and re-render the static and animated metro map images to pick up the upstream rowspan bbox-shrink fix ([@pinin4fjords](https://github.com/pinin4fjords)).

conf/modules.config

@@ -227,6 +227,7 @@ process {
             "--reml ${meta.params.dream_reml}",
             ((meta.params.seed != null) ? "--seed $meta.params.seed" : ""),
             "--apply_voom ${meta.params.dream_apply_voom}",
+            ((meta.params.round_digits != null && meta.params.round_digits > 0) ? "--round_digits $meta.params.round_digits" : ""),
             ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking")
         ].join(' ').trim() }
     }
@@ -246,6 +247,7 @@ process {
             "--reml ${meta.params.dream_reml}",
             ((meta.params.seed != null) ? "--seed $meta.params.seed" : ""),
             "--apply_voom ${meta.params.dream_apply_voom}",
+            ((meta.params.round_digits != null && meta.params.round_digits > 0) ? "--round_digits $meta.params.round_digits" : ""),
             ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking")
         ].join(' ').trim() }
     }
@@ -374,7 +376,16 @@ process {
             def min_n = meta.params?.decoupler_min_n ?: 5
             def methods = meta.params?.decoupler_methods ?: 'mlm'
 
-            "--min_n ${min_n} --transpose TRUE --ensembl_ids TRUE --methods ${methods} --features_id_col ${features_id} --features_symbol_col ${features_symbol} --column ${meta.params.differential_fc_column}"
+            [
+                "--min_n ${min_n}",
+                "--transpose TRUE",
+                "--ensembl_ids TRUE",
+                "--methods ${methods}",
+                "--features_id_col ${features_id}",
+                "--features_symbol_col ${features_symbol}",
+                "--column ${meta.params.differential_fc_column}",
+                ((meta.params.round_digits != null && meta.params.round_digits > 0) ? "--round_digits ${meta.params.round_digits}" : "")
+            ].join(' ').trim()
         }
     }
 

conf/test/generic_matrix/generic_matrix_dream.config

@@ -30,5 +30,6 @@ params {
     report_contributors = 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
 
     // Other
-    round_digits = 3
+    round_digits = 2
+    seed         = 10
 }

conf/test/maxquant/maxquant.config

@@ -25,4 +25,5 @@ params {
     // Proteus
     proteus_measurecol_prefix = 'LFQ intensity'
     round_digits              = 4
+    seed                      = 10
 }

conf/test/rnaseq/rnaseq_dream_complex.config

@@ -24,5 +24,6 @@ params {
     report_contributors = 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
 
     // Other
-    round_digits = 3
+    round_digits = 2
+    seed         = 10
 }

conf/test/rnaseq/rnaseq_dream_decoupler_complex.config

@@ -24,5 +24,6 @@ params {
     report_contributors = 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
 
     // Other
-    round_digits = 3
+    round_digits = 2
+    seed         = 10
 }

conf/test_paramsheet.yaml

@@ -158,7 +158,8 @@
     PhD student
     Institute of Microbiology
     University of Smallville
-  round_digits: 3
+  round_digits: 2
+  seed: 10
 
 - paramset_name: test_rnaseq_dream
   include: test_paramsheet/rnaseq_dream,test_paramsheet/rnaseq_testdata_complex
@@ -172,7 +173,8 @@
     PhD student
     Institute of Microbiology
     University of Smallville
-  round_digits: 3
+  round_digits: 2
+  seed: 10
 
 - paramset_name: test_affy_limma_gprofiler2
   include: test_paramsheet/affy_limma_gprofiler2,test_paramsheet/affy_testdata
@@ -183,6 +185,8 @@
   differential_max_qval: 0.05
   differential_min_fold_change: 1.5
   gprofiler2_organism: "mmusculus"
+  round_digits: 2
+  seed: 10
 
 - paramset_name: test_rnaseq_propd_grea
   include: test_paramsheet/rnaseq_propd_grea,test_paramsheet/rnaseq_testdata

docs/usage.md

@@ -79,6 +79,33 @@ The `file` column in this example is used to specify the data file associated wi
 
 This is a numeric matrix file, comma or tab-separated, with features as rows and observations in columns. The features correspond to the supplied feature set. The parameters `--observations_id_col` and `--features_id_col` define which of the associated fields should be matched in those inputs.
 
+For example, with the default `--observations_id_col sample` and `--features_id_col gene_id`, the sample identifiers in the samplesheet should match the matrix column names:
+
+```csv title="samplesheet.csv"
+sample,condition
+sample_1,control
+sample_2,control
+sample_3,treatment
+```
+
+The feature identifiers should match the row identifiers in the matrix:
+
+```tsv title="features.tsv"
+gene_id	gene_name
+ENSG00000141510	TP53
+ENSG00000171862	PTEN
+ENSG00000139618	BRCA2
+```
+
+The matrix can then use those feature identifiers as rows and sample identifiers as columns:
+
+```tsv title="matrix.tsv"
+gene_id	sample_1	sample_2	sample_3
+ENSG00000141510	42	51	96
+ENSG00000171862	108	99	87
+ENSG00000139618	15	18	44
+```
+
 #### Outputs from nf-core/rnaseq and other tximport-processed results
 
 The nf-core RNAseq workflow incorporates [tximport](https://bioconductor.org/packages/release/bioc/html/tximport.html) for producing quantification matrices. From [version 3.12.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2), it additionally provides transcript/gene length matrices which can be directly consumed by DESeq2 to model length bias across samples.

modules.json

@@ -47,8 +47,8 @@
                     },
                     "decoupler/decoupler": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
-                        "installed_by": ["differential_functional_enrichment"]
+                        "git_sha": "95a5fb210d019a00acef7ce1febde2e448e0508e",
+                        "installed_by": ["differential_functional_enrichment", "modules"]
                     },
                     "deseq2/differential": {
                         "branch": "master",
@@ -128,7 +128,7 @@
                     },
                     "variancepartition/dream": {
                         "branch": "master",
-                        "git_sha": "87e0996ad70cb449019c505fd5f53f6594e26e4f",
+                        "git_sha": "95a5fb210d019a00acef7ce1febde2e448e0508e",
                         "installed_by": ["abundance_differential_filter", "modules"]
                     },
                     "zip": {