Integrate subworkflows into pipeline

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [[#431](https://github.com/nf-core/differentialabundance/pull/431)] - Add differential and functional subworkflows. ([@suzannejin](https://github.com/suzannejin), co-authored by [@bjlang](https://github.com/bjlang) and [@caraiz2001](https://github.com/caraiz2001), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#421](https://github.com/nf-core/differentialabundance/pull/421)] - Add immunedeconv module ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#380](https://github.com/nf-core/differentialabundance/pull/380)] - Replace local filter_diff_table module with nf-core one, and create nf-tests for tabular_to_gsea_chip. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Added software version check in nf-tests and gene biotype column check in `.Rmd` ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords))
@@ -32,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [[#431](https://github.com/nf-core/differentialabundance/pull/431)] - Replace the calls to differential and functional analysis modules by subworkflows. ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#410](https://github.com/nf-core/differentialabundance/pull/410)] - Update contrasts file format to allow yaml ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#374](https://github.com/nf-core/differentialabundance/pull/374)] - Update all modules and subworkflows ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#348](https://github.com/nf-core/differentialabundance/pull/348)] - Update test_full profile matrix file and indentation of profiles in nextflow.config ([@nschcolnicov](https://github.com/nschcolnicov), review by [@WackerO](https://github.com/WackerO) and [@pinin4fjords](https://github.com/pinin4fjords))

conf/modules.config

@@ -188,7 +188,7 @@ process {
             "--shrink_lfc $params.deseq2_shrink_lfc",
             "--cores $params.deseq2_cores",
             "--subset_to_contrast_samples $params.differential_subset_to_contrast_samples",
-            ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking"),
+            ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking"),  // TODO check what is the impact of blocking for NORM
         ].join(' ').trim() }
     }
 
@@ -238,6 +238,38 @@ process {
         ].join(' ').trim() }
     }
 
+    withName: LIMMA_NORM {
+        ext.prefix = 'all'
+        publishDir = [
+            [
+                path: { "${params.outdir}/tables/processed_abundance" },
+                mode: params.publish_dir_mode,
+                pattern: '*.{normalised_counts}.tsv'
+            ],
+        ]
+        ext.when = params.limma_use_voom
+        ext.args = { [
+            "--probe_id_col \"${params.features_id_col}\"",
+            "--sample_id_col \"${params.observations_id_col}\"",
+            "--ndups \"${params.limma_ndups}\"",
+            "--spacing \"${params.limma_spacing}\"",
+            "--block \"${params.limma_block}\"",
+            "--correlation ${params.limma_correlation}",
+            "--method \"${params.limma_method}\"",
+            "--proportion ${params.limma_proportion}",
+            "--stdev.coef.lim \"${params.limma_stdev_coef_lim}\"",
+            "--trend ${params.limma_trend}",
+            "--robust ${params.limma_robust}",
+            "--winsor.tail.p \"${params.limma_winsor_tail_p}\"",
+            "--p.value ${params.limma_p_value}",
+            "--lfc ${params.limma_lfc}",
+            "--confint ${params.limma_confint}",
+            "--subset_to_contrast_samples $params.differential_subset_to_contrast_samples",
+            "--use_voom \"${params.limma_use_voom}\"",
+            ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking"),
+        ].join(' ').trim() }
+    }
+
     withName: LIMMA_DIFFERENTIAL {
         ext.prefix = { "${meta.id}" }
         publishDir = [
@@ -494,7 +526,7 @@ process {
         ]
     }
 
-    withName: 'TABULAR_TO_GSEA_CHIP' {
+    withName: 'CUSTOM_TABULARTOGSEACHIP' {
         publishDir = [
             enabled: false
         ]

modules.json

@@ -17,23 +17,28 @@
                     },
                     "custom/filterdifferentialtable": {
                         "branch": "master",
-                        "git_sha": "833a65446ea117d092d4940f098236b6766e7aac",
-                        "installed_by": ["modules"]
+                        "git_sha": "045f0fbb65edaff2ca5002754dfa767d93551c66",
+                        "installed_by": ["abundance_differential_filter", "modules"]
                     },
                     "custom/matrixfilter": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "custom/tabulartogseachip": {
+                        "branch": "master",
+                        "git_sha": "7900e49fb84969a2479ecfbeef7bcbe296513c90",
+                        "installed_by": ["differential_functional_enrichment"]
+                    },
                     "custom/tabulartogseacls": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "git_sha": "c835e1647a2e16237ae9d1db3d27351297f290c5",
+                        "installed_by": ["differential_functional_enrichment", "modules"]
                     },
                     "custom/tabulartogseagct": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "git_sha": "c835e1647a2e16237ae9d1db3d27351297f290c5",
+                        "installed_by": ["differential_functional_enrichment", "modules"]
                     },
                     "deseq2/differential": {
                         "branch": "master",
@@ -47,13 +52,13 @@
                     },
                     "gprofiler2/gost": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "git_sha": "6506b7bc2a369f0c21dc4fbc5e8d2af6c3e1a90b",
+                        "installed_by": ["differential_functional_enrichment", "modules"]
                     },
                     "gsea/gsea": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "git_sha": "6506b7bc2a369f0c21dc4fbc5e8d2af6c3e1a90b",
+                        "installed_by": ["differential_functional_enrichment", "modules"]
                     },
                     "gunzip": {
                         "branch": "master",
@@ -67,8 +72,18 @@
                     },
                     "limma/differential": {
                         "branch": "master",
-                        "git_sha": "136f443c0a6d5c526410c7c9b73ce51ef457c341",
-                        "installed_by": ["modules"]
+                        "git_sha": "784b3a38aeafe9bb7e38f1369704dd5e6bcaf9f0",
+                        "installed_by": ["abundance_differential_filter", "modules"]
+                    },
+                    "propr/grea": {
+                        "branch": "master",
+                        "git_sha": "138b2c45dde12b2075d6fe15a5d374b48d166d4a",
+                        "installed_by": ["differential_functional_enrichment"]
+                    },
+                    "propr/propd": {
+                        "branch": "master",
+                        "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
+                        "installed_by": ["abundance_differential_filter"]
                     },
                     "proteus/readproteingroups": {
                         "branch": "master",
@@ -114,6 +129,16 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "abundance_differential_filter": {
+                        "branch": "master",
+                        "git_sha": "2b977a47af8a319f6ef6e7b918e7bb64babbaa04",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "differential_functional_enrichment": {
+                        "branch": "master",
+                        "git_sha": "6506b7bc2a369f0c21dc4fbc5e8d2af6c3e1a90b",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",