rewriting output directories - publishDir, unifying outputs in a commonsense way, adding these to each modules nextflow.config file, NOT tested yet

Author: number-25

conf/test.config

@@ -12,6 +12,7 @@
 
 includeConfig "../modules/local/isoquant/isoquant/test_nextflow.config"
 includeConfig "../modules/local/gffcompare/gffcompare/nextflow.config"
+includeConfig "../modules/local/nanoq/nanoq/nextflow.config"
 
 params {
     config_profile_name             = 'Test profile'

conf/test_full.config

@@ -11,6 +11,7 @@
 */
 
 includeConfig "../modules/local/gffcompare/gffcompare/nextflow.config"
+includeConfig "../modules/local/nanoq/nanoq/nextflow.config"
 
 params {
     config_profile_name        = 'Full test profile'
@@ -61,7 +62,7 @@ params {
     extra_stringtie_options         = null
     skip_jaffal                     = true
     skip_jaffal_download            = true
-    jaffal_reference                = null
+    jaffal_reference                = "assets/fulltest_data/for_jaffal"
     // TRANSCRIPT QUANTIFICATION
     skip_transcript_quantification  = false
     skip_oarfish                    = false

modules.json

@@ -20,20 +20,8 @@
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     },
-                    "ucsc/bedclip": {
-                        "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
-                    "ucsc/bedgraphtobigwig": {
-                        "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
-                    "untar": {
-                        "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["modules"]
                     }
                 }
             },

modules/local/alfred/qc/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'ALFRED' {
+        publishDir = [
+        path: { "${params.outdir}/mapping_qc/alfred/${meta.id}_${meta.replicate}" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}

modules/local/alfred/transpose/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'TRANSPOSE' {
+        publishDir = [
+        path: { "${params.outdir}/mapping_qc/alfred/${meta.id}_${meta.replicate}" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}

modules/local/bambu/bambu/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'BAMBU' {
+        publishDir = [
+        path: { "${params.outdir}/transcript_reconstruction/bambu/${meta.id}_${meta.replicate}" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}

modules/local/bedtools/bam_to_bedgraph/main.nf

@@ -5,7 +5,6 @@ process BAM_TO_BEDGRAPH {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_2':
         'biocontainers/bedtools:2.31.1--hf5e1c6e_2' }"
-    //publishDir "
 
     input:
     tuple val(meta), path(bam)

modules/local/bedtools/bam_to_bedgraph/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'BAM_TO_BEDGRAPH' {
+        publishDir = [
+        path: { "${params.outdir}/mapping_visualisation/${meta.id}_${meta.replicate}" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}

modules/local/bedtools/jaccard/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'BEDTOOLS_JACCARD' {
+        publishDir = [
+        path: { "${params.outdir}/transcriptome_assessment/jaccard/${meta.id}_${meta.replicate}" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}

modules/local/cramino/cramino/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'CRAMINO' {
+        publishDir = [
+        path: { "${params.outdir}/mapping_qc/cramino/${meta.id}_${meta.replicate}" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}