From d5d77b7a09fb530e6bb41c0264479f47317f40d5 Mon Sep 17 00:00:00 2001
From: Jens Preussner <jens.preussner@mpi-bn.mpg.de>
Date: Mon, 30 Apr 2018 16:47:41 +0200
Subject: [PATCH] Small bug fixes

---
 environment.yml          | 2 +-
 src/auxiliary.snake      | 5 ++++-
 src/createSCE_kallisto.R | 2 +-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 7e7bf89..81d24ec 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,7 +9,7 @@ dependencies:
   - salmon
   - kallisto
   #- htstream
-  #- umis
+  - umis
   - r-magrittr
   - r-data.table
   - r-readr
diff --git a/src/auxiliary.snake b/src/auxiliary.snake
index 46a34aa..35cfefe 100644
--- a/src/auxiliary.snake
+++ b/src/auxiliary.snake
@@ -27,7 +27,10 @@ def find_nested_key(d, k):
   return(None)
 
 def find_metadata_files(wildcards):
-  metadata = [config['samplesheet']['file'], join(config['dirs']['tables'], 'salmon.txt')]
+  metadata = [config['samplesheet']['file']]
+  if config['action']['quantification'] == 'salmon':
+    metadata.extend([config['samplesheet']['file'], join(config['dirs']['tables'], 'salmon.txt')])
+  
   if config['action']['clean']:
     metadata.extend([join(config['dirs']['tables'], 'htstream.txt')])
   if config['action']['demultiplex']:
diff --git a/src/createSCE_kallisto.R b/src/createSCE_kallisto.R
index 3246c75..63dc24b 100644
--- a/src/createSCE_kallisto.R
+++ b/src/createSCE_kallisto.R
@@ -66,7 +66,7 @@ if (!is.null(metadata_files)) {
   metadata_ <- lapply(metadata_files, function(p) metadata <- data.table::fread(input = p, sep = "\t", header = T, stringsAsFactors = T, na.strings = "NA"))
   metadata <- Reduce(function(a, b) dplyr::left_join(a, b, by = snakemake@config$samplesheet$index), metadata_)
 
-  m <- match(colnames(expression[[1]]), make.names(metadata[, snakemake@config$samplesheet$index]))
+  m <- match(colnames(expression[[1]]), make.names(metadata[[which(colnames(metadata) == snakemake@config$samplesheet$index)]]))
   colData_ <- as.data.frame(metadata[na.omit(m), ])
   rownames(colData_) <- make.names(colData_[, snakemake@config$samplesheet$index])
 } else {