From f7f61d07eeb0f0c7df230dd30cfdcf29cc9a46ea Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Jun 2018 13:27:39 +0200
Subject: [PATCH] change collect to toList in nf files and run tests with
 multiple fastq

---
 README.md                                       | 9 +++++++++
 src/nf_modules/Bowtie2/bowtie2.nf               | 4 ++--
 src/nf_modules/Bowtie2/tests/mapping_paired.nf  | 2 +-
 src/nf_modules/Bowtie2/tests/mapping_single.nf  | 2 +-
 src/nf_modules/Bowtie2/tests/tests.sh           | 4 ++--
 src/nf_modules/Kallisto/kallisto.nf             | 6 +++---
 src/nf_modules/Kallisto/tests/mapping_paired.nf | 2 +-
 src/nf_modules/Kallisto/tests/mapping_single.nf | 2 +-
 src/nf_modules/Kallisto/tests/tests.sh          | 4 ++--
 9 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index 301ac36..31bce23 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 fe19db8..095d85f 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 c6c79b8..048db49 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 70c55b7..c5c7f58 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 888e698..55e88ed 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 885f6ae..0af1fc8 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 447577d..71b9f47 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 69e3a6f..2a46cbe 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 3d49f1e..f83a4ca 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"
 
-- 
GitLab