diff tools/myTools/bin/test-data/pipe.nf @ 1:7e5c71b2e71f draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/myTools/bin/test-data/pipe.nf	Wed Dec 22 16:00:34 2021 +0000
@@ -0,0 +1,332 @@
+#!/usr/bin/env nextflow
+
+params.expressions = "$baseDir/input_data/expressions.csv"
+params.network = "$baseDir/input_data/network.sif"
+params.samples = "$baseDir/input_data/samples.txt"
+params.alpha = 0.9
+params.internal_control="$baseDir/input_data/internal_control.txt"
+params.undesired = 'resistant'
+params.desired = 'sensitive'
+params.filter ="strict"
+
+
+params.kmeans_min_val = 2
+params.kmeans_max_val = 10
+
+
+params.num_nodes = 4 // that have expression data
+params.num_states = 1000
+
+
+params.mut = false
+
+process sfa_exp {
+    publishDir 'results', mode: 'copy', overwrite: true
+    input: 
+    path "expressions.csv" from params.expressions
+    path "network.sif" from params.network
+
+    output: 
+    path 'attrs_exp.txt' into records_expattr
+
+    script:
+    """
+    SFA_exp_attr.py network.sif expressions.csv attrs_exp.txt
+    """
+}
+
+process get_exp_internal_control_nodes {  
+    publishDir 'results', mode: 'copy', overwrite: true
+    
+    input:
+    path 'attrs_exp.txt' from records_expattr
+    path "internal_control.txt" from params.internal_control
+
+    output:
+    path 'attrs_exp_internal_controls.txt' into records_exp_icns
+    
+    script:
+    """
+    get_RONs.py attrs_exp.txt internal_control.txt
+    """
+    
+}
+
+
+
+process insilico_inits {
+
+    output: 
+    path 'init.txt' into records_insilicoinit
+
+    script:
+    """
+    generate_basal_states.py $params.num_states $params.num_nodes init.txt attr -1,0,1
+    """
+}
+process insilico {
+    publishDir 'results', mode: 'copy', overwrite: true
+    input:
+    path 'expressions.csv' from params.expressions
+    path 'network.sif' from params.network
+    path 'samples.txt' from params.samples
+    path 'init.txt' from records_insilicoinit
+ 
+    output:
+    path 'attrs_insilico*' into records_insilico
+ 
+    script:
+ 
+    """
+    SFA_insilico.py "network.sif" "expressions.csv" "samples.txt" init.txt $params.alpha
+    """
+}
+
+process getFVS {
+    publishDir 'results', mode: 'copy', overwrite: true
+
+    input:
+    path 'network.sif' from params.network
+ 
+    output:
+    path 'fvs.txt' into records_fvs
+    script:
+    """
+    FVS_run.py network.sif
+    """
+}
+process perturbation_inits {
+    publishDir 'results', mode: 'copy', overwrite: true
+    input:
+    path "fvs.txt" from records_fvs
+    // path 'fvs.txt' from records3a
+    
+    output:
+    path 'fvs_init.txt' into records_pert_inits
+    
+
+    script:
+    """
+    generate_perts.py fvs.txt fvs_init.txt pert -1,0,1
+    """
+}
+process sfa_perts {
+    publishDir 'results', mode: 'copy', overwrite: true
+    input:
+    path 'expressions.csv' from params.expressions
+    path 'network.sif' from params.network
+    path 'samples.txt' from params.samples
+    path "fvs.txt" from records_fvs
+    path 'fvs_init.txt' from records_pert_inits
+ 
+    output:
+    path 'pert*' into records_perts
+ 
+    script:
+    """
+    SFA_virtscreen.py network.sif expressions.csv $params.undesired samples.txt fvs.txt fvs_init.txt $params.alpha
+    
+    """
+}
+
+process check_icns{
+    publishDir 'results', mode: 'copy', overwrite: true
+    input:
+    path 'attrs_exp_internal_controls.txt' from records_exp_icns
+    path 'samples.txt' from params.samples
+
+    output:
+    path 'internal_control_nodes_exp_attrs.pdf' into records_icn_check
+
+    script:
+    """
+    module load R/3.6.3
+    icn_check1.R attrs_exp_internal_controls.txt samples.txt
+    """
+    
+}
+
+process kmeans_opt {
+    publishDir 'results', mode: 'copy', overwrite: true
+
+    input:
+    path 'attrs_exp.txt' from records_expattr
+    path 'attrs_insilico*' from records_insilico
+ 
+    output:
+    env ELBOW into records_elbow
+    env SILHOUETTE into records_silhouette
+    path '*.pdf' into records_silplots
+    path '*.png' into records_elbowplots
+    
+    shell:
+    """
+    datasets=\$(ls -m attr* | sed 's/ //g')
+    echo \$datasets
+    export SILHOUETTE=\$(silhouette_metric.py \$datasets results/ $params.kmeans_max_val)
+    export ELBOW=\$(elbow_metric.py \$datasets results/ $params.kmeans_max_val)
+    """
+}
+process kmeans {
+    // this one checks to see if clusters and phenotypes match up
+    publishDir 'results', mode: 'copy', overwrite: true
+    input:
+    val ELBOW from records_elbow
+    val SILHOUETTE from records_silhouette
+    path 'attrs_exp.txt' from records_expattr
+    path 'attrs_insilico*' from records_insilico
+    path 'samples.txt' from params.samples
+
+    output:
+    path 'kmeans.txt' into records_kmeans
+
+    script:
+    if (ELBOW==SILHOUETTE)
+        """
+        datasets=\$(ls -m attr* | sed 's/ //g')
+        kmeans.py $ELBOW \$datasets
+        """
+
+    else if (ELBOW<SILHOUETTE)
+        """
+        datasets=\$(ls -m attr* | sed 's/ //g')
+        kmeans.py $ELBOW \$datasets
+        """
+    else if (SILHOUETTE<ELBOW)
+        """
+        datasets=\$(ls -m attr* | sed 's/ //g')
+        kmeans.py $SILHOUETTE \$datasets
+        """
+
+}
+
+process classification {
+    publishDir 'results', mode: 'copy', overwrite: true
+    input:
+    path 'kmeans.txt' from records_kmeans
+    path 'pert*' from records_perts
+    path 'samples.txt' from params.samples
+    path 'attrs_exp.txt' from records_expattr
+    path 'attrs_insilico*' from records_insilico
+    output:
+    path 'class_*' into records_classification
+    
+    script:
+    """
+    export train=\$(ls -m attr* | sed 's/ //g')
+    for x in pert*
+    do
+        NB.py \$train \$x kmeans.txt 
+        RF.py \$train \$x kmeans.txt
+        SVM.py \$train \$x kmeans.txt
+    done
+    """
+}
+process consensus {
+    
+    publishDir 'results', mode: 'copy', overwrite: true
+    input:
+    path '*' from records_classification
+    path 'kmeans.txt' from records_kmeans
+    path 'samples.txt' from params.samples
+    
+    output:
+    path 'crit1perts.txt' into records_consensus
+    
+    script:
+    """
+    datasets=\$(ls -m class_* | tr -d '[:space:]')
+
+    export desired_sample=\$(grep $params.desired samples.txt | head -1 | sed 's/\t.*//')
+    export desired_cluster=\$(grep \$desired_sample kmeans.txt | head -1 | sed 's/.*\s//')
+    get_clusterconsensus.py \$datasets \$desired_cluster
+    """
+    
+}
+
+process internal_control_node_analysis {  
+    publishDir 'results', mode: 'copy', overwrite: true
+    
+    input:
+    path 'pert*' from records_perts
+    path 'crit1perts.txt' from records_consensus
+    path "internal_control.txt" from params.internal_control
+    
+    output:
+    path '*_internal_controls.txt' into records_pert_icns
+    
+    script:
+    """
+    for x in pert*
+    do
+    echo \$x
+    get_RONs_getperts.py \$x "internal_control.txt" 'crit1perts.txt'
+    done
+    """
+    
+}
+
+
+process filtering_by_icn {  
+    publishDir 'results', mode: 'copy', overwrite: true
+    
+    input:
+    path 'attrs_exp_internal_controls.txt' from records_exp_icns
+    path 'pert_logss*' from records_pert_icns
+    path 'samples.txt' from params.samples
+
+    output:
+    path '*_filtered_perturbations.txt' into records_filtered_perts
+    
+    script:
+    """
+    module load R/3.6.3
+    for x in pert_logss*
+    do
+    crit2.R attrs_exp_internal_controls.txt samples.txt \$x $params.desired $params.undesired $params.filter
+    done
+    """
+    
+}
+
+process extract_perts {  
+    publishDir 'results', mode: 'copy', overwrite: true
+    
+    input:
+    path 'fvs_init.txt' from records_pert_inits
+    path "fvs.txt" from records_fvs
+    path '*_filtered_perturbations.txt' from records_filtered_perts
+
+
+    output:
+    path 'extract_perts.txt' into records_extracted_perts
+    
+    script:
+    """
+    for x in *_filtered_perturbations.txt
+    do
+    get_perts.py fvs_init.txt fvs.txt \$x
+    done
+    """
+    
+}
+
+process translate_perts {  
+    publishDir 'results', mode: 'copy', overwrite: true
+    
+    input:
+    path 'extract_perts.txt' from records_extracted_perts
+
+
+    output:
+    path 'perts_translated.txt' into records_translated_perts
+    
+    script:
+    """
+    module load R/3.6.3
+    pertanalysis.R extract_perts.txt
+    """
+    
+}
+
+