change collect to toList in nf files and run tests with multiple fastq

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

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

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

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

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"
 

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

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

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

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"