rsem: fix tests

src/nf_modules/rsem/quantification_single.nf

@@ -24,7 +24,7 @@ process mapping_fastq {
 
   input:
   set file_id, file(reads) from fastq_files
-  file index from index_files.toList()
+  file index from index_files.collect()
 
   output:
   file "*" into count_files
@@ -37,7 +37,6 @@ process mapping_fastq {
     }
   }
 """
-ls -l
 rsem-calculate-expression --bowtie2 \
 --bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
 --bowtie2-sensitivity-level "very_sensitive" \

src/nf_modules/rsem/tests.sh

@@ -9,7 +9,7 @@
   -c src/nf_modules/rsem/quantification_single.config \
   -profile docker \
   --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
   -resume
 
 ./nextflow src/nf_modules/rsem/quantification_paired.nf \
@@ -32,7 +32,7 @@ if [ -x "$(command -v singularity)" ]; then
   -c src/nf_modules/rsem/quantification_single.config \
   -profile docker \
   --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
   -resume
 
 ./nextflow src/nf_modules/rsem/quantification_paired.nf \