Change: flashweave pipeline will not support bootstrapping

segrelab · Mar 2, 2021 · 775f89f · 775f89f
1 parent ddbe778
commit 775f89f
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diff --git a/micone/config/configs/network_inference.toml b/micone/config/configs/network_inference.toml
@@ -152,9 +152,6 @@
   [[network_inference.direct.flashweave.input]]
     datatype = "sample_metadata"
     format = ["tsv"]
-  [[network_inference.direct.flashweave.input]]
-    datatype = "otu_bootstrap"
-    format = ["boot"]
   [[network_inference.direct.flashweave.parameters]]
     process = "flashweave"
     ncpus = 1
@@ -165,11 +162,6 @@
     datatype = "interaction_table"
     format = ["tsv"]
     location = "**/*_corr.tsv"
-  [[network_inference.direct.flashweave.output]]
-    datatype = "interaction_bootstrap"
-    format = ["boot"]
-    location = "**/*_corr.boot"
-
 
 [network_inference.direct.mldm]
   env = "micone-mldm"

diff --git a/micone/pipelines/src/network_inference/direct/flashweave/process.config b/micone/pipelines/src/network_inference/direct/flashweave/process.config
@@ -8,7 +8,6 @@ flashweave {
 params {
     output_dir = "{{ output_dir }}"
     otudata = "{{ input['otu_table'] }}"
-    otu_bootstrap = "{{ input['otu_bootstrap'] }}"
     sample_metadata = "{{ input['sample_metadata'] }}"
 
     ncpus = flashweave.ncpus

diff --git a/micone/pipelines/src/network_inference/direct/flashweave/process.nf b/micone/pipelines/src/network_inference/direct/flashweave/process.nf
@@ -2,7 +2,6 @@
 
 // Initialize variables
 def otudata = params.otudata
-def otu_bootstrap = params.otu_bootstrap
 def sample_metadata = file(params.sample_metadata)
 def output_dir = file(params.output_dir)
 
@@ -26,18 +25,6 @@ Channel
     ) }
     .set { chnl_otudata }
 
-Channel
-    .fromPath(otu_bootstrap)
-    .ifEmpty {exit 1, "Otu files not found"}
-    .map { tuple(
-        (it.getParent().getParent().baseName + '_' + it.getParent().baseName + '_' + it.baseName),
-        it.getParent().getParent().baseName,
-        it.getParent().baseName,
-        it
-    ) }
-    .set { chnl_otudata_boot }
-
-
 // Processes
 
 process flashweave_graph {
@@ -60,24 +47,3 @@ process flashweave_corr {
     script:
     {{ export_gml }}
 }
-
-process flashweave_graph_boot {
-    tag "${id}"
-    input:
-    set val(id), val(dataset), val(level), file(otu_file) from chnl_otudata_boot
-    output:
-    set val(id), file(otu_file), file('*_network.gml') into chnl_graph_boot
-    script:
-    {{ flashweave }}
-}
-
-process flashweave_corr_boot {
-    tag "${id}"
-    publishDir "${output_dir}/${dataset}/${level}", saveAs: { fname -> fname.split('.tsv')[0] + '.boot' }, mode: 'copy', overwrite: true
-    input:
-    set val(id), file(otu_file), file(network_file) from chnl_graph_boot
-    output:
-    set val(id), file('*_corr.tsv') into chnl_corr_boot
-    script:
-    {{ export_gml }}
-}