working optional beer (#63)

* working optional beer
matsengrp · Jun 12, 2023 · 46e9dec · 46e9dec
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diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,9 @@
+# Nextflow
+.nextflow*
+**/*Attic*
+**/*_ignore*
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/README.md b/README.md
@@ -3,9 +3,6 @@ A Nextflow pipeline for Common Phage Immuno-Precipitation Sequencing experiments
 See the [Documentation](https://matsengrp.github.io/phippery/introduction.html)
 for more details and usage examples.
 
-[![nextflow]()]()
-[![Build Status]()]()
-
 ## Quickstart 
 
 Install `Nextflow` by using the following command: 
@@ -21,6 +18,6 @@ Launch the pipeline execution with the following command:
 
     nextflow run matsengrp/phip-flow -profile docker
 
-Note: the [Dockerfile](docker/Dockerfile) contains all the required dependencies. 
+Note: the ``phippery`` [Dockerfile](https://github.com/matsengrp/phippery/blob/main/Dockerfile) contains all the required dependencies. 
 Add the `-profile docker` to enable the containerized execution to the 
 example command line shown below. 
diff --git a/bin/run_BEER.Rscript b/bin/run_BEER.Rscript
@@ -0,0 +1,47 @@
+#!/usr/bin/env Rscript
+
+library(beer)
+library(PhIPData)
+library(dplyr)
+
+# input from the edgeR process
+edgeR_out = readRDS("PhIPData.rds")
+
+# For more on running BEER
+# see http://www.bioconductor.org/packages/release/bioc/html/beer.html
+
+### Named vector specifying where we want to store the summarized MCMC output
+### NULL indicates that the output should not be stored.
+print("Setting up BEER")
+assay_locations <- c(
+  phi = "beer_fc_marg", 
+  phi_Z = "beer_fc_cond", 
+  Z = "beer_prob", 
+  c = "sampleInfo", 
+  pi = "sampleInfo"
+)
+
+print("Running BEER::brew")
+beer_out <- brew(edgeR_out, assay.names = assay_locations)
+
+## Define matrix of peptides that were run in BEER
+print("Getting matrix of peptides that were run")
+was_run <- matrix(rep(beer_out$group != "beads", each = nrow(beer_out)), 
+                  nrow = nrow(beer_out))
+
+## Identify super-enriched peptides
+## These peptides were in samples that were run, but have missing posterior 
+## probabilities
+print("Identifying super-enriched peptides")
+are_se <- was_run & is.na(assay(beer_out, "beer_prob"))
+
+## Enriched peptides are peptides with:
+## - posterior probability > 0.5, OR
+## - super-enriched peptides
+print("Rerunning BEER")
+assay(beer_out, "beer_hits") <- assay(beer_out, "beer_prob") > 0.5 | are_se
+
+write.csv(assays(beer_out)$beer_prob, file="beer_prob.csv")
+write.csv(assays(beer_out)$beer_hits, file="beer_hits.csv")
+
+saveRDS(edgeR_out, "PhIPData.rds")
diff --git a/data/conf/column_names.yaml b/data/conf/column_names.yaml
diff --git a/...simulated-example/NGS/expa/sample_0.fastq → ...simulated-example/NGS/expa/sample_0.fastq b/...simulated-example/NGS/expa/sample_0.fastq → ...simulated-example/NGS/expa/sample_0.fastq
diff --git a/...simulated-example/NGS/expa/sample_1.fastq → ...simulated-example/NGS/expa/sample_1.fastq b/...simulated-example/NGS/expa/sample_1.fastq → ...simulated-example/NGS/expa/sample_1.fastq
diff --git a/...imulated-example/NGS/expa/sample_10.fastq → ...imulated-example/NGS/expa/sample_10.fastq b/...imulated-example/NGS/expa/sample_10.fastq → ...imulated-example/NGS/expa/sample_10.fastq
diff --git a/...imulated-example/NGS/expa/sample_11.fastq → ...imulated-example/NGS/expa/sample_11.fastq b/...imulated-example/NGS/expa/sample_11.fastq → ...imulated-example/NGS/expa/sample_11.fastq
diff --git a/...simulated-example/NGS/expa/sample_2.fastq → ...simulated-example/NGS/expa/sample_2.fastq b/...simulated-example/NGS/expa/sample_2.fastq → ...simulated-example/NGS/expa/sample_2.fastq
diff --git a/...simulated-example/NGS/expa/sample_3.fastq → ...simulated-example/NGS/expa/sample_3.fastq b/...simulated-example/NGS/expa/sample_3.fastq → ...simulated-example/NGS/expa/sample_3.fastq
diff --git a/...simulated-example/NGS/expa/sample_4.fastq → ...simulated-example/NGS/expa/sample_4.fastq b/...simulated-example/NGS/expa/sample_4.fastq → ...simulated-example/NGS/expa/sample_4.fastq
diff --git a/...simulated-example/NGS/expa/sample_5.fastq → ...simulated-example/NGS/expa/sample_5.fastq b/...simulated-example/NGS/expa/sample_5.fastq → ...simulated-example/NGS/expa/sample_5.fastq
diff --git a/...simulated-example/NGS/expa/sample_6.fastq → ...simulated-example/NGS/expa/sample_6.fastq b/...simulated-example/NGS/expa/sample_6.fastq → ...simulated-example/NGS/expa/sample_6.fastq
diff --git a/...simulated-example/NGS/expa/sample_7.fastq → ...simulated-example/NGS/expa/sample_7.fastq b/...simulated-example/NGS/expa/sample_7.fastq → ...simulated-example/NGS/expa/sample_7.fastq
diff --git a/...simulated-example/NGS/expa/sample_8.fastq → ...simulated-example/NGS/expa/sample_8.fastq b/...simulated-example/NGS/expa/sample_8.fastq → ...simulated-example/NGS/expa/sample_8.fastq
diff --git a/...simulated-example/NGS/expa/sample_9.fastq → ...simulated-example/NGS/expa/sample_9.fastq b/...simulated-example/NGS/expa/sample_9.fastq → ...simulated-example/NGS/expa/sample_9.fastq
diff --git a/data/simulated-example/nextflow.config → data/misc/simulated-example/nextflow.config b/data/simulated-example/nextflow.config → data/misc/simulated-example/nextflow.config
diff --git a/data/simulated-example/peptide_table.csv → .../misc/simulated-example/peptide_table.csv b/data/simulated-example/peptide_table.csv → .../misc/simulated-example/peptide_table.csv
diff --git a/...ated-example/peptide_table_replicates.csv → ...ated-example/peptide_table_replicates.csv b/...ated-example/peptide_table_replicates.csv → ...ated-example/peptide_table_replicates.csv
diff --git a/data/simulated-example/run_phip_flow.sh → data/misc/simulated-example/run_phip_flow.sh b/data/simulated-example/run_phip_flow.sh → data/misc/simulated-example/run_phip_flow.sh
diff --git a/data/simulated-example/sample_table.csv → data/misc/simulated-example/sample_table.csv b/data/simulated-example/sample_table.csv → data/misc/simulated-example/sample_table.csv
diff --git a/data/pan-cov-example-with-beads-no-lib/peptide_table.csv b/data/pan-cov-example-with-beads-no-lib/peptide_table.csv
diff --git a/data/pan-cov-example-with-beads/NGS/4A-rep1-27-library_S27_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/4A-rep1-27-library_S27_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/NGS/4A-rep2-22_S49_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/4A-rep2-22_S49_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/NGS/4B-rep1-22_S22_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/4B-rep1-22_S22_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/NGS/4B-rep1-27-library_S26_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/4B-rep1-27-library_S26_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/NGS/ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/NGS/ex8-rep2-42_S87_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/ex8-rep2-42_S87_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/NGS/expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/NGS/rep1-42_S42_L001_R1_001.fastq.gz.test.gz b/data/pan-cov-example-with-beads/NGS/rep1-42_S42_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example-with-beads/peptide_table.csv b/data/pan-cov-example-with-beads/peptide_table.csv
diff --git a/data/pan-cov-example/NGS/20-05-14-cov2-ex4a/4A-rep1-27-library_S27_L001_R1_001_sub.fastq.gz b/data/pan-cov-example/NGS/20-05-14-cov2-ex4a/4A-rep1-27-library_S27_L001_R1_001_sub.fastq.gz
diff --git a/data/pan-cov-example/NGS/20-05-14-cov2-ex4a/4A-rep2-18_S45_L001_R1_001.fastq.gz b/data/pan-cov-example/NGS/20-05-14-cov2-ex4a/4A-rep2-18_S45_L001_R1_001.fastq.gz
diff --git a/data/pan-cov-example/NGS/20-05-15-cov2-ex4b/4B-rep1-18_S18_L001_R1_001.fastq.gz b/data/pan-cov-example/NGS/20-05-15-cov2-ex4b/4B-rep1-18_S18_L001_R1_001.fastq.gz
diff --git a/data/pan-cov-example/NGS/20-05-15-cov2-ex4b/4B-rep1-27-library_S26_L001_R1_001_sub.fastq.gz b/data/pan-cov-example/NGS/20-05-15-cov2-ex4b/4B-rep1-27-library_S26_L001_R1_001_sub.fastq.gz
diff --git a/data/pan-cov-example/NGS/20-05-27-cov2-ex5a/rep1-15_S15_L001_R1_001.fastq.gz b/data/pan-cov-example/NGS/20-05-27-cov2-ex5a/rep1-15_S15_L001_R1_001.fastq.gz
diff --git a/data/pan-cov-example/NGS/20-06-02-cov2-ex5b/ex5b-rep1-15_S15_L001_R1_001.fastq.gz b/data/pan-cov-example/NGS/20-06-02-cov2-ex5b/ex5b-rep1-15_S15_L001_R1_001.fastq.gz
diff --git a/...-library_S27_L001_R1_001.fastq.gz.test.gz → ...-library_S27_L001_R1_001.fastq.gz.test.gz b/...-library_S27_L001_R1_001.fastq.gz.test.gz → ...-library_S27_L001_R1_001.fastq.gz.test.gz
diff --git a/...-rep2-22_S49_L001_R1_001.fastq.gz.test.gz → ...-rep2-22_S49_L001_R1_001.fastq.gz.test.gz b/...-rep2-22_S49_L001_R1_001.fastq.gz.test.gz → ...-rep2-22_S49_L001_R1_001.fastq.gz.test.gz
diff --git a/...-rep1-22_S22_L001_R1_001.fastq.gz.test.gz → ...-rep1-22_S22_L001_R1_001.fastq.gz.test.gz b/...-rep1-22_S22_L001_R1_001.fastq.gz.test.gz → ...-rep1-22_S22_L001_R1_001.fastq.gz.test.gz
diff --git a/...-library_S26_L001_R1_001.fastq.gz.test.gz → ...-library_S26_L001_R1_001.fastq.gz.test.gz b/...-library_S26_L001_R1_001.fastq.gz.test.gz → ...-library_S26_L001_R1_001.fastq.gz.test.gz
diff --git a/...beads-35_S87_L001_R1_001.fastq.gz.test.gz → ...beads-35_S87_L001_R1_001.fastq.gz.test.gz b/...beads-35_S87_L001_R1_001.fastq.gz.test.gz → ...beads-35_S87_L001_R1_001.fastq.gz.test.gz
diff --git a/...-rep2-42_S87_L001_R1_001.fastq.gz.test.gz → ...-rep2-42_S87_L001_R1_001.fastq.gz.test.gz b/...-rep2-42_S87_L001_R1_001.fastq.gz.test.gz → ...-rep2-42_S87_L001_R1_001.fastq.gz.test.gz
diff --git a/...-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz → ...-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz b/...-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz → ...-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz
diff --git a/.../rep1-42_S42_L001_R1_001.fastq.gz.test.gz → .../rep1-42_S42_L001_R1_001.fastq.gz.test.gz b/.../rep1-42_S42_L001_R1_001.fastq.gz.test.gz → .../rep1-42_S42_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example/sample_table.csv b/data/pan-cov-example/sample_table.csv
diff --git a/...n-cov-example-with-beads/sample_table.csv → ...ample/sample_table_with_beads_and_lib.csv b/...n-cov-example-with-beads/sample_table.csv → ...ample/sample_table_with_beads_and_lib.csv
@@ -1,9 +1,9 @@
 technical_replicate_id,submitted_by,library_batch,control_status,sample_ID,sample_type,species,participant_ID,age,sex,race,days_from_symptom_onset,patient_status,source,pandemic_status,fastq_filepath
-273,hannah,MEGSUB,library,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example-with-beads/NGS/4B-rep1-27-library_S26_L001_R1_001.fastq.gz.test.gz
-572,mackenzie,MEGSUB,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example-with-beads/NGS/expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz
-247,caitlin,SUB2,library,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example-with-beads/NGS/4A-rep1-27-library_S27_L001_R1_001.fastq.gz.test.gz
-725,caitlin,SUB2,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example-with-beads/NGS/ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz
-90,caitlin,MEGSUB,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example-with-beads/NGS/rep1-42_S42_L001_R1_001.fastq.gz.test.gz
-382,caitlin,SUB2,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example-with-beads/NGS/ex8-rep2-42_S87_L001_R1_001.fastq.gz.test.gz
-269,hannah,MEGSUB,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example-with-beads/NGS/4B-rep1-22_S22_L001_R1_001.fastq.gz.test.gz
-242,caitlin,SUB2,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example-with-beads/NGS/4A-rep2-22_S49_L001_R1_001.fastq.gz.test.gz
+273,hannah,MEGSUB,library,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/4B-rep1-27-library_S26_L001_R1_001.fastq.gz.test.gz
+572,mackenzie,MEGSUB,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz
+247,caitlin,SUB2,library,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/4A-rep1-27-library_S27_L001_R1_001.fastq.gz.test.gz
+725,caitlin,SUB2,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz
+90,caitlin,MEGSUB,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example/NGS/rep1-42_S42_L001_R1_001.fastq.gz.test.gz
+382,caitlin,SUB2,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example/NGS/ex8-rep2-42_S87_L001_R1_001.fastq.gz.test.gz
+269,hannah,MEGSUB,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example/NGS/4B-rep1-22_S22_L001_R1_001.fastq.gz.test.gz
+242,caitlin,SUB2,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example/NGS/4A-rep2-22_S49_L001_R1_001.fastq.gz.test.gz
diff --git a/...xample-with-beads-no-lib/sample_table.csv → ...xample/sample_table_with_beads_no_lib.csv b/...xample-with-beads-no-lib/sample_table.csv → ...xample/sample_table_with_beads_no_lib.csv
@@ -1,7 +1,7 @@
 technical_replicate_id,submitted_by,library_batch,control_status,sample_ID,sample_type,species,participant_ID,age,sex,race,days_from_symptom_onset,patient_status,source,pandemic_status,fastq_filepath
-572,mackenzie,MEGSUB,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example-with-beads-no-lib/NGS/expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz
-725,caitlin,SUB2,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example-with-beads-no-lib/NGS/ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz
-90,caitlin,MEGSUB,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example-with-beads-no-lib/NGS/rep1-42_S42_L001_R1_001.fastq.gz.test.gz
-382,caitlin,SUB2,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example-with-beads-no-lib/NGS/ex8-rep2-42_S87_L001_R1_001.fastq.gz.test.gz
-269,hannah,MEGSUB,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example-with-beads-no-lib/NGS/4B-rep1-22_S22_L001_R1_001.fastq.gz.test.gz
-242,caitlin,SUB2,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example-with-beads-no-lib/NGS/4A-rep2-22_S49_L001_R1_001.fastq.gz.test.gz
+572,mackenzie,MEGSUB,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz
+725,caitlin,SUB2,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz
+90,caitlin,MEGSUB,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example/NGS/rep1-42_S42_L001_R1_001.fastq.gz.test.gz
+382,caitlin,SUB2,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example/NGS/ex8-rep2-42_S87_L001_R1_001.fastq.gz.test.gz
+269,hannah,MEGSUB,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example/NGS/4B-rep1-22_S22_L001_R1_001.fastq.gz.test.gz
+242,caitlin,SUB2,empirical,45,serum,human,13a,NA,NA,NA,NA,healthy adult,Chu lab,pre,data/pan-cov-example/NGS/4A-rep2-22_S49_L001_R1_001.fastq.gz.test.gz
diff --git a/data/pan-cov-example/sample_table_with_beads_one_emp.csv b/data/pan-cov-example/sample_table_with_beads_one_emp.csv
@@ -0,0 +1,4 @@
+technical_replicate_id,submitted_by,library_batch,control_status,sample_ID,sample_type,species,participant_ID,age,sex,race,days_from_symptom_onset,patient_status,source,pandemic_status,fastq_filepath
+572,mackenzie,MEGSUB,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz
+725,caitlin,SUB2,beads_only,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,data/pan-cov-example/NGS/ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz
+90,caitlin,MEGSUB,empirical,80,ACD plasma,human,32C,36.0,Male,White,30.0,conv outpatient 30d,Helen Chu,pandemic,data/pan-cov-example/NGS/rep1-42_S42_L001_R1_001.fastq.gz.test.gz
diff --git a/main.nf b/main.nf
@@ -23,8 +23,8 @@ nextflow.enable.dsl = 2
 /*
  * Define the default parameters - example data get's run by default
  */ 
-params.sample_table     = "$baseDir/data/pan-cov-example/sample_table.csv"
-if (params.sample_table != "$baseDir/data/pan-cov-example/sample_table.csv")
+params.sample_table     = "$baseDir/data/pan-cov-example/sample_table_with_beads_and_lib.csv"
+if (params.sample_table != "$baseDir/data/pan-cov-example/sample_table_with_beads_and_lib.csv")
     params.reads_prefix = "$launchDir"
 else
     params.reads_prefix = "$baseDir"

diff --git a/nextflow.config b/nextflow.config
@@ -60,7 +60,10 @@ params{
 
     run_cpm_enr_workflow = false
     run_zscore_fit_predict = false
-    run_edgeR_save_rds = false
+    run_edgeR = true
+
+    // WARNING: This functionality has not been fully tested
+    run_BEER = false
 
 
     /*
@@ -103,7 +106,7 @@ process {
     // Default for any processes which do not match the selectors below
     container = 'quay.io/hdc-workflows/phippery:1.1.4'
 
-    withName: run_edgeR {
+    withName: 'run_edgeR|run_BEER' {
         container = 'quay.io/biocontainers/bioconductor-beer:1.2.0--r42hdfd78af_0'
     }
 

diff --git a/workflows/edgeR.nf b/workflows/edgeR.nf
diff --git a/workflows/edgeR_BEER.nf b/workflows/edgeR_BEER.nf
@@ -0,0 +1,99 @@
+// Run external statistical analysis tools
+
+
+// EXTRACT WIDE CSV
+process to_csv {
+    input: path phip_data
+    output: 
+    tuple path(phip_data), path("*.csv")
+    shell:
+    """
+    phippery to-wide-csv -o dataset $phip_data
+    """
+}
+
+// RUN BEER
+process run_edgeR {
+    // publishDir "$params.results/rds_data/", mode: 'copy', overwrite: true
+    input:
+    tuple path(phip_data), path(phip_data_csvs)
+    output:
+    tuple path(phip_data), path("edgeR*.csv"), path("PhIPData.rds"), val("edgeR")
+    shell:    
+    """
+    run_edgeR.Rscript ${params.edgeR_threshold}
+    """
+}
+//mv PhIPData.rds ${params.dataset_prefix}.rds
+
+process run_BEER {
+    // publishDir "$params.results/rds_data/", mode: 'copy', overwrite: true
+    input:
+    tuple path(phip_data), path("*"), path(edgeR_rds), val(method)
+    output:
+    tuple path(phip_data), path("beer*.csv"), path("PhIPData.rds"), val("BEER")
+    shell:    
+    """
+    run_BEER.Rscript
+    """
+
+}
+
+process publish_rds {
+    publishDir "$params.results/rds_data/", mode: 'copy', overwrite: true
+    input:
+    tuple path(phip_data), path(csvs), path(rds_data), val(method)
+    output:
+    path rds_data
+    """
+    echo publishing $rds_data 
+    """
+}
+
+// APPEND EDGER RESULTS INTO XARRAY DATASET
+process append_assay_csvs_to_xarray {
+    input:
+    tuple path(phip_data), path(csvs), path(rds_data), val(method)
+    output:
+    path "${method}.phip"
+    shell:
+    """
+    #!/usr/bin/env python3
+
+    import glob
+    from phippery.utils import *
+    import pandas as pd
+
+    ds = load("$phip_data")
+    for csv in glob.glob("*.csv"):
+        df = pd.read_csv(csv, index_col=0)
+        table_name = csv.split(".")[0]
+        add_enrichment_layer_from_array(
+            ds, df.values, new_table_name=table_name
+        )
+
+    dump(ds, "${method}.phip") 
+    """
+}
+
+workflow edgeR_BEER_workflows {
+    take:
+        ds
+    main:
+
+    if ( params.run_BEER )
+        ds | to_csv \
+            | run_edgeR \
+            | run_BEER \
+            | (append_assay_csvs_to_xarray & publish_rds)
+    else
+        ds | to_csv \
+            | run_edgeR \
+            | (append_assay_csvs_to_xarray & publish_rds)
+
+    emit:
+        append_assay_csvs_to_xarray.out
+
+}
+
+