small fixes to allow main_coda.nf to run

nf-core · Jul 26, 2024 · e3fde5b · e3fde5b
1 parent bf70167
commit e3fde5b
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Showing 8 changed files with 73 additions and 12 deletions.
diff --git a/assets/tools_samplesheet.csv b/assets/tools_samplesheet.csv
@@ -1,6 +1,7 @@
 pathway_name,diff_method,args_diff,enr_diff_method,args_enr_diff,cor_method,args_cor,enr_cor_method,args_enr_cor,sel_method,args_sel
-diff_prop,propd, --adjacency true --permutation 100 --fixseed true, , ,,, , ,,
-filtered_pcor,propd, --adjacency true --permutation 100 --fixseed true, , ,propr,  --permutation 10 --adjacency true --cutoff_min 0.005 --cutoff_max 0.5 --cutoff_interval 0.01 --metric pcor.bshrink, , , filtervar,
+diff_prop,propd,--group_col fase --adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 100 --fixseed true, , ,,, , ,,
+diff_prop_noperm,propd,--group_col fase --adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 0 --fixseed true, , ,,, , ,,
+filtered_pcor,propd,--group_col fase --adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 100 --fixseed true, , ,propr,  --permutation 10 --adjacency true --cutoff_min 0.005 --cutoff_max 0.5 --cutoff_interval 0.01 --metric pcor.bshrink, , , filtervar,
 prop,, , , ,propr,  --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true --metric rho --permutation 100 --adjacency true, , , ,
-diff_grea,propd,--group_col fase --adjacency true --permutation 10,grea, --permutation 10, , , , ,,
+diff_grea,propd,--group_col fase --adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 10 --fixseed true,grea, --permutation 10, , , , ,,
 deseq2,deseq2,,gsea,,,,,,,
diff --git a/conf/modules.config b/conf/modules.config
@@ -481,4 +481,54 @@ process {
             enabled: false
         ]
     }
+
+    withName: "PROPR"{
+        ext.args = { "${meta.args_cor}" == "null" ? '' : "${meta.args_cor}" }
+        publishDir = [
+            path: { "${params.outdir}/correlation_analysis/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: "PROPD"{
+        ext.args = { "${meta.args_diff}" == "null" ? '' : "${meta.args_diff}" }
+        publishDir = [
+            path: { "${params.outdir}/differential_analysis/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "FILTERVAR"{
+        ext.args = { "${meta.args_cor}" == "null" ? '' : "${meta.args_cor}" }
+        publishDir = [
+            path: { "${params.outdir}/variable_selection/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "GREA_DIFF"{
+        ext.args = { "${meta.args_enr_diff}" == "null" ? '' : "${meta.args_enr_diff}" }
+        publishDir = [
+            path: { "${params.outdir}/enrichment_differential/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "GREA_COR"{
+        ext.args = { "${meta.args_enr_cor}" == "null" ? '' : "${meta.args_enr_cor}" }
+        publishDir = [
+            path: { "${params.outdir}/enrichment_correlation/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "MYGENE" {
+        ext.args = { [
+            "--columname ${params.features_id_col}",
+        ].join(' ').trim() }
+    }
 }
diff --git a/main_coda.nf b/main_coda.nf
@@ -2,15 +2,15 @@
 // include { PROPR_PROPD        } from '../../../modules/nf-core/propr/propd/main'
 // include { PROPR_GREA         } from '../../../modules/nf-core/propr/grea/main'
 // include { MYGENE             } from '../../../modules/nf-core/mygene/main'
-include { EXPERIMENTAL        } from './subworkflows/experimental/main.nf'
+include { EXPERIMENTAL        } from './subworkflows/local/experimental/main.nf'
 include { fromSamplesheet } from 'plugin/nf-validation'
 
 
 // These are local files from my Bachelor Thesis project, I am creating the ch_samples_and_matrix
 // manually for testing but it should be be provided by the processing section of nf-core/differentialabundance
-Counts_ch = Channel.fromPath("../YMC/counts_sin0.csv")
+Counts_ch = Channel.fromPath(params.matrix)
 
-Sample_ch = Channel.fromPath("../YMC/samplesheet_RCvsOX.csv")
+Sample_ch = Channel.fromPath(params.input)
     .map{ it -> [[id: 'YMC'], it]}
 
 ch_samples_and_matrix = Sample_ch.combine(Counts_ch)

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -58,6 +58,16 @@
                     "default": "counts",
                     "description": "Type of abundance measure used, platform-dependent",
                     "fa_icon": "fas fa-keyboard"
+                },
+                "tools": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/csv",
+                    "schema": "assets/schema_tools.json",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml)$",
+                    "description": "Path to comma-separated file containing samplesheet",
+                    "help_text": "This file defines possible combinations of tools, which are to be run by the pipeline"
                 }
             }
         },

diff --git a/subworkflows/local/correlation/main.nf b/subworkflows/local/correlation/main.nf
@@ -1,6 +1,6 @@
 
 // include nf-core modules
-include {PROPR_PROPR as PROPR} from "../../modules/nf-core/propr/propr/main.nf"
+include {PROPR_PROPR as PROPR} from "../../../modules/nf-core/propr/propr/main.nf"
 
 
 workflow CORRELATION {

diff --git a/subworkflows/local/differential/main.nf b/subworkflows/local/differential/main.nf
@@ -1,5 +1,5 @@
 // include modules
-include {PROPR_PROPD as PROPD} from "../../modules/nf-core/propr/propd/main.nf"
+include {PROPR_PROPD as PROPD} from "../../../modules/nf-core/propr/propd/main.nf"
 
 
 workflow DIFFERENTIAL {

diff --git a/subworkflows/local/enrichment/main.nf b/subworkflows/local/enrichment/main.nf
@@ -1,8 +1,8 @@
 // include modules
 
-include { PROPR_GREA as GREA_DIFF } from "../../modules/nf-core/propr/grea/main.nf"
-include { PROPR_GREA as GREA_COR } from "../../modules/nf-core/propr/grea/main.nf"
-include { MYGENE } from "../../modules/nf-core/mygene/main.nf"
+include { PROPR_GREA as GREA_DIFF } from "../../../modules/nf-core/propr/grea/main.nf"
+include { PROPR_GREA as GREA_COR  } from "../../../modules/nf-core/propr/grea/main.nf"
+include { MYGENE } from "../../../modules/nf-core/mygene/main.nf"
 
 
 workflow ENRICHMENT {

diff --git a/subworkflows/local/variable_selection/main.nf b/subworkflows/local/variable_selection/main.nf
@@ -1,5 +1,5 @@
 // include modules
-include { FILTERVAR } from "../../modules/local/filtervar/main.nf"
+include { FILTERVAR } from "../../../modules/local/filtervar/main.nf"
 
 workflow VARIABLE_SELECTION {
     take: