Fix: publishDir folder names for NI workflow

segrelab · Sep 30, 2021 · 5656b85 · 5656b85
1 parent 21d8508
commit 5656b85
Show file tree

Hide file tree

Showing 11 changed files with 22 additions and 11 deletions.
diff --git a/micone/pipelines/modules/network_inference/bootstrap/pvalue.nf b/micone/pipelines/modules/network_inference/bootstrap/pvalue.nf
@@ -3,7 +3,7 @@ include { getHierarchy } from '../../../functions/functions.nf'
 process pvalues {
     label 'sparcc'
     tag "${meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -13,6 +13,7 @@ process pvalues {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         ncpus = params.network_inference.bootstrap['pvalue']['ncpus']
         template 'network_inference/bootstrap/calculate_pvalues.sh'
 }
diff --git a/micone/pipelines/modules/network_inference/correlation/pearson.nf b/micone/pipelines/modules/network_inference/correlation/pearson.nf
@@ -3,7 +3,7 @@ include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 process pearson {
     label 'micone'
     tag "${new_meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${new_meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -17,6 +17,7 @@ process pearson {
         new_meta.network_inference = 'pearson'
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         ncpus = params.network_inference.correlation['pearson']['ncpus']
         template 'network_inference/correlation/pearson.py'
 }
diff --git a/micone/pipelines/modules/network_inference/correlation/propr.nf b/micone/pipelines/modules/network_inference/correlation/propr.nf
@@ -3,7 +3,7 @@ include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 process propr {
     label 'propr'
     tag "${new_meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${new_meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -16,6 +16,7 @@ process propr {
         new_meta = updateMeta(meta)
         new_meta.network_inference = 'propr'
         String task_process = "${task.process}"
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         f = getHierarchy(task_process)
         ncpus = params.network_inference.correlation['propr']['ncpus']
         template 'network_inference/correlation/propr.R'

diff --git a/micone/pipelines/modules/network_inference/correlation/sparcc.nf b/micone/pipelines/modules/network_inference/correlation/sparcc.nf
@@ -3,7 +3,7 @@ include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 process sparcc {
     label 'sparcc'
     tag "${new_meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${new_meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -17,6 +17,7 @@ process sparcc {
         new_meta.network_inference = 'sparcc'
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         ncpus = params.network_inference.correlation['sparcc']['ncpus']
         iterations = params.network_inference.correlation['sparcc']['iterations']
         template 'network_inference/correlation/sparcc.sh'

diff --git a/micone/pipelines/modules/network_inference/correlation/spearman.nf b/micone/pipelines/modules/network_inference/correlation/spearman.nf
@@ -3,7 +3,7 @@ include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 process spearman {
     label 'micone'
     tag "${new_meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${new_meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -17,6 +17,7 @@ process spearman {
         new_meta.network_inference = 'spearman'
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         ncpus = params.network_inference.correlation['spearman']['ncpus']
         template 'network_inference/correlation/spearman.py'
 }
diff --git a/micone/pipelines/modules/network_inference/direct/export_gml.nf b/micone/pipelines/modules/network_inference/direct/export_gml.nf
@@ -3,7 +3,7 @@ include { getHierarchy } from '../../../functions/functions.nf'
 process export_gml {
     label 'flashweave'
     tag "${meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -13,5 +13,6 @@ process export_gml {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         template 'network_inference/direct/export_gml.py'
 }
diff --git a/micone/pipelines/modules/network_inference/direct/flashweave.nf b/micone/pipelines/modules/network_inference/direct/flashweave.nf
@@ -3,7 +3,7 @@ include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 process flashweave {
     label 'flashweave'
     tag "${new_meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${new_meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -17,6 +17,7 @@ process flashweave {
         new_meta.network_inference = 'flashweave'
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         ncpus = params.network_inference.direct['flashweave']['ncpus']
         sensitive = params.network_inference.direct['flashweave']['sensitive']
         heterogeneous = params.network_inference.direct['flashweave']['heterogeneous']

diff --git a/micone/pipelines/modules/network_inference/direct/mldm.nf b/micone/pipelines/modules/network_inference/direct/mldm.nf
@@ -3,7 +3,7 @@ include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 process mldm {
     label 'mldm'
     tag "${new_meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${new_meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -17,6 +17,7 @@ process mldm {
         new_meta.network_inference = 'mldm'
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         Z_mean = params.network_inference.direct['mldm']['Z_mean']
         max_iteration = params.network_inference.direct['mldm']['max_iteration']
         template 'network_inference/direct/mldm.R'

diff --git a/micone/pipelines/modules/network_inference/direct/spieceasi.nf b/micone/pipelines/modules/network_inference/direct/spieceasi.nf
@@ -3,7 +3,7 @@ include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 process spieceasi {
     label 'spieceasi'
     tag "${new_meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${new_meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/${f[1]}/${f[2]}/${directory}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -17,6 +17,7 @@ process spieceasi {
         new_meta.network_inference = 'spieceasi'
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}"
         method = params.network_inference.direct['spieceasi']['method']
         ncpus = params.network_inference.direct['spieceasi']['ncpus']
         nreps = params.network_inference.direct['spieceasi']['nreps']

diff --git a/micone/pipelines/modules/network_inference/network/make_network_with_pvalue.nf b/micone/pipelines/modules/network_inference/network/make_network_with_pvalue.nf
@@ -3,7 +3,7 @@ include { getHierarchy } from '../../../functions/functions.nf'
 process make_network_with_pvalue {
     label 'micone'
     tag "${meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/network/${f[1]}/${meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/network/${f[1]}/${directory}/${meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -13,6 +13,7 @@ process make_network_with_pvalue {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}-${meta.network_inference}"
         metadata_file = params.network_inference.network['make_network_with_pvalue']['metadata_file']
         interaction_threshold = params.network_inference.network['make_network_with_pvalue']['interaction_threshold']
         pvalue_threshold = params.network_inference.network['make_network_with_pvalue']['pvalue_threshold']

diff --git a/micone/pipelines/modules/network_inference/network/make_network_without_pvalue.nf b/micone/pipelines/modules/network_inference/network/make_network_without_pvalue.nf
@@ -3,7 +3,7 @@ include { getHierarchy } from '../../../functions/functions.nf'
 process make_network_without_pvalue {
     label 'micone'
     tag "${meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/network/${f[1]}/${meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/network/${f[1]}/${directory}/${meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -13,6 +13,7 @@ process make_network_without_pvalue {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        directory = "${meta.denoise_cluster}-${meta.chimera_checking}-${meta.tax_assignment}-${meta.tax_level}-${meta.network_inference}"
         metadata_file = params.network_inference.network['make_network_without_pvalue']['metadata_file']
         interaction_threshold = params.network_inference.network['make_network_without_pvalue']['interaction_threshold']
         template 'network_inference/network/make_network_without_pvalue.py'