Fix: Minor issues in the network_inference workflow

segrelab · May 27, 2021 · d6de68c · d6de68c
1 parent 1242cd6
commit d6de68c
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Showing 6 changed files with 9 additions and 7 deletions.
diff --git a/micone/pipelines/modules/network_inference/bootstrap/resample.nf b/micone/pipelines/modules/network_inference/bootstrap/resample.nf
@@ -4,7 +4,7 @@ process resample {
     input:
         tuple val(meta), file(otu_file), file(obs_metadata), file(sample_metadata), file(children_map)
     output:
-        tuple val(meta), file(otu_file), file('bootstraps/*.boot.temp'), file(obsmeta_file), file(samplemeta_file), file(children_file)
+        tuple val(meta), file(otu_file), file('bootstraps/*_otu.boot'), file(obs_metadata), file(sample_metadata), file(children_map)
     script:
         ncpus = params.network_inference.bootstrap['resample']['ncpus']
         bootstraps = params.network_inference.bootstrap['resample']['bootstraps']

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}/${f[0]}/${f[1]}/${f[2]}/${meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/network/${f[1]}/${meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -13,7 +13,7 @@ process make_network_with_pvalue {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
-        metadata = params.network_inference.network['make_network_with_pvalue']['metadata']
+        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']
         template 'network_inference/network/make_network_with_pvalue.py'

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}/${f[0]}/${f[1]}/${f[2]}/${meta.id}",
+    publishDir "${params.output_dir}/${f[0]}/network/${f[1]}/${meta.id}",
         mode: 'copy',
         overwrite: true
     input:
@@ -13,7 +13,7 @@ process make_network_without_pvalue {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
-        metadata = params.network_inference.network['make_network_without_pvalue']['metadata']
+        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'
 }
diff --git a/micone/pipelines/templates/network_inference/correlation/sparcc.sh b/micone/pipelines/templates/network_inference/correlation/sparcc.sh
@@ -14,4 +14,6 @@ function do_fastspar {
         --threads 1
 }
 
+export -f do_fastspar
+
 find . -name "*_otu.boot" | parallel -j ${ncpus} do_fastspar
diff --git a/micone/pipelines/templates/network_inference/network/make_network_with_pvalue.py b/micone/pipelines/templates/network_inference/network/make_network_with_pvalue.py
@@ -49,7 +49,7 @@ def create_cmetadata():
     BASE_NAME = "${meta.id}"
     CORR_FILE = "${corr_file}"
     PVALUE_FILE = "${pvalue_file}"
-    META_FILE = "${metadata}"
+    META_FILE = "${metadata_file}"
     OBSMETA_FILE = "${obs_metadata}"
     CHILDREN_FILE = "${children_map}"
     INTERACTION_THRESHOLD = ${interaction_threshold}

diff --git a/micone/pipelines/templates/network_inference/network/make_network_without_pvalue.py b/micone/pipelines/templates/network_inference/network/make_network_without_pvalue.py
@@ -44,7 +44,7 @@ def create_cmetadata():
 if __name__ == "__main__":
     BASE_NAME = "${meta.id}"
     CORR_FILE = "${corr_file}"
-    META_FILE = "${metadata}"
+    META_FILE = "${metadata_file}"
     OBSMETA_FILE = "${obs_metadata}"
     CHILDREN_FILE = "${children_map}"
     INTERACTION_THRESHOLD = ${interaction_threshold}