diff --git a/README.md b/README.md
index 301ac36a4e9161ab4e95c94c09acc1c24b38dfe6..31bce23528aeee9c88cafc50d10e1e8d123ea2b5 100644
--- a/README.md
+++ b/README.md
@@ -42,6 +42,15 @@ src/nf_modules/file_handle/0.1.1/docker_init.sh
 
 ## Running the tests
 
+```sh
+cd data
+git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
+cp data/tiny_dataset/fastq/tiny_R1.fastq data/tiny_dataset/fastq/tiny2_R1.fastq
+cp data/tiny_dataset/fastq/tiny_R2.fastq data/tiny_dataset/fastq/tiny2_R2.fastq
+cp data/tiny_dataset/fastq/tiny_S.fastq data/tiny_dataset/fastq/tiny2_S.fastq
+nextflow src/nf_test.nf -c src/nf_test.config --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+```
+
 Explain how to run the automated tests for this system
 
 ### Break down into end to end tests
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index fe19db848fa739c404ebc55bf3372b99ae85b953..095d85ff62d70d14d204e09e6fb2eaf5244ea1b7 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -63,7 +63,7 @@ process mapping_fastq {
 
   input:
   set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*.bam" into bam_files
@@ -106,7 +106,7 @@ process mapping_fastq {
 
   input:
   file reads from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*.bam" into bam_files
diff --git a/src/nf_modules/Bowtie2/tests/mapping_paired.nf b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
index c6c79b8d034bca0152fedbd17a3a2cdd967b1fc3..048db49b684e18326323621a7873b6db4b0c5071 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
@@ -20,7 +20,7 @@ process mapping_fastq {
 
   input:
   set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*.bam" into bam_files
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
index 70c55b76a4c2bc642f1ad50d35c8bff1d835b532..c5c7f585514c7ba97da98a660c02964a4d5a91b1 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -19,7 +19,7 @@ process mapping_fastq {
 
   input:
   file reads from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*.bam" into bam_files
diff --git a/src/nf_modules/Bowtie2/tests/tests.sh b/src/nf_modules/Bowtie2/tests/tests.sh
index 888e6988265859c920e75a37bb1eb0ae819aa91b..55e88edb145255aea143a632aea6e4b3cb5f2833 100644
--- a/src/nf_modules/Bowtie2/tests/tests.sh
+++ b/src/nf_modules/Bowtie2/tests/tests.sh
@@ -7,11 +7,11 @@ nextflow src/nf_modules/Bowtie2/tests/mapping_single.nf \
   -c src/nf_modules/Bowtie2/bowtie2.config \
   -profile docker \
   --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
 
 nextflow src/nf_modules/Bowtie2/tests/mapping_paired.nf \
   -c src/nf_modules/Bowtie2/bowtie2.config \
   -profile docker \
   --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
 
diff --git a/src/nf_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
index 885f6ae337715e80f2300ece63a2a9e88194e5c7..0af1fc84a80b9552297a5c7968f0e2aaf64bc65e 100644
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ b/src/nf_modules/Kallisto/kallisto.nf
@@ -12,7 +12,7 @@ log.info "fasta files : ${params.fasta}"
 
 Channel
   .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
   .set { fasta_file }
 
 process index_fasta {
@@ -60,7 +60,7 @@ process mapping_fastq {
 
   input:
   set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*" into counts_files
@@ -105,7 +105,7 @@ process mapping_fastq {
 
   input:
   file reads from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*" into count_files
diff --git a/src/nf_modules/Kallisto/tests/mapping_paired.nf b/src/nf_modules/Kallisto/tests/mapping_paired.nf
index 447577dd2c5c05c8b7c1afb111ef06689f7bc5d4..71b9f471968fb7cb6a73871d6c88e7a96c4d37d7 100644
--- a/src/nf_modules/Kallisto/tests/mapping_paired.nf
+++ b/src/nf_modules/Kallisto/tests/mapping_paired.nf
@@ -20,7 +20,7 @@ process mapping_fastq {
 
   input:
   set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*" into counts_files
diff --git a/src/nf_modules/Kallisto/tests/mapping_single.nf b/src/nf_modules/Kallisto/tests/mapping_single.nf
index 69e3a6fdcafe5d1804a96cd482f6b5ff4cf50bfe..2a46cbe6dc1274a2c46044f01a54e43c981126ad 100644
--- a/src/nf_modules/Kallisto/tests/mapping_single.nf
+++ b/src/nf_modules/Kallisto/tests/mapping_single.nf
@@ -24,7 +24,7 @@ process mapping_fastq {
 
   input:
   file reads from fastq_files
-  file index from index_files.collect()
+  file index from index_files.toList()
 
   output:
   file "*" into count_files
diff --git a/src/nf_modules/Kallisto/tests/tests.sh b/src/nf_modules/Kallisto/tests/tests.sh
index 3d49f1ec534dcd3dd66a196663069614cac0494a..f83a4cacb2caaa66490b00ba224205af13e92967 100644
--- a/src/nf_modules/Kallisto/tests/tests.sh
+++ b/src/nf_modules/Kallisto/tests/tests.sh
@@ -7,11 +7,11 @@ nextflow src/nf_modules/Kallisto/tests/mapping_single.nf \
   -c src/nf_modules/Kallisto/kallisto.config \
   -profile docker \
   --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
 
 nextflow src/nf_modules/Kallisto/tests/mapping_paired.nf \
   -c src/nf_modules/Kallisto/kallisto.config \
   -profile docker \
   --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"