From 5386a28643cebb8418cca477a63ca0f3a4ac5353 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 31 Aug 2018 17:06:08 +0200
Subject: [PATCH] nf_modules: fix tests.sh to use local nextflow bin
---
src/nf_modules/BEDtools/tests.sh | 2 +-
src/nf_modules/FastQC/tests.sh | 4 ++--
src/nf_modules/HTSeq/tests.sh | 2 +-
src/nf_modules/MultiQC/tests.sh | 4 ++--
src/nf_modules/RSEM/tests.sh | 6 +++---
src/nf_modules/SAMtools/tests.sh | 8 ++++----
src/nf_modules/SRAtoolkit/tests.sh | 2 +-
src/nf_modules/UrQt/tests.sh | 4 ++--
src/nf_modules/cutadapt/tests.sh | 8 ++++----
9 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/src/nf_modules/BEDtools/tests.sh b/src/nf_modules/BEDtools/tests.sh
index 4d6bda0d..632ba5bf 100755
--- a/src/nf_modules/BEDtools/tests.sh
+++ b/src/nf_modules/BEDtools/tests.sh
@@ -1,4 +1,4 @@
-nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
+./nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
-c src/nf_modules/BEDtools/fasta_from_bed.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
diff --git a/src/nf_modules/FastQC/tests.sh b/src/nf_modules/FastQC/tests.sh
index b103ac74..de58b102 100755
--- a/src/nf_modules/FastQC/tests.sh
+++ b/src/nf_modules/FastQC/tests.sh
@@ -1,9 +1,9 @@
-nextflow src/nf_modules/FastQC/fastqc_paired.nf \
+./nextflow src/nf_modules/FastQC/fastqc_paired.nf \
-c src/nf_modules/FastQC/fastqc_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/FastQC/fastqc_single.nf \
+./nextflow src/nf_modules/FastQC/fastqc_single.nf \
-c src/nf_modules/FastQC/fastqc_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq"
diff --git a/src/nf_modules/HTSeq/tests.sh b/src/nf_modules/HTSeq/tests.sh
index f7255c23..4a2b5ceb 100755
--- a/src/nf_modules/HTSeq/tests.sh
+++ b/src/nf_modules/HTSeq/tests.sh
@@ -1,4 +1,4 @@
-nextflow src/nf_modules/HTSeq/htseq.nf \
+./nextflow src/nf_modules/HTSeq/htseq.nf \
-c src/nf_modules/HTSeq/htseq.config \
-profile docker \
--gtf "data/tiny_dataset/annot/tiny.gff" \
diff --git a/src/nf_modules/MultiQC/tests.sh b/src/nf_modules/MultiQC/tests.sh
index 40b6522e..0e38a8e9 100755
--- a/src/nf_modules/MultiQC/tests.sh
+++ b/src/nf_modules/MultiQC/tests.sh
@@ -1,9 +1,9 @@
-nextflow src/nf_modules/MultiQC/multiqc_paired.nf \
+./nextflow src/nf_modules/MultiQC/multiqc_paired.nf \
-c src/nf_modules/MultiQC/multiqc_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/MultiQC/multiqc_single.nf \
+./nextflow src/nf_modules/MultiQC/multiqc_single.nf \
-c src/nf_modules/MultiQC/multiqc_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq"
diff --git a/src/nf_modules/RSEM/tests.sh b/src/nf_modules/RSEM/tests.sh
index c57c8c4f..7d56b790 100755
--- a/src/nf_modules/RSEM/tests.sh
+++ b/src/nf_modules/RSEM/tests.sh
@@ -1,16 +1,16 @@
-nextflow src/nf_modules/RSEM/indexing.nf \
+./nextflow src/nf_modules/RSEM/indexing.nf \
-c src/nf_modules/RSEM/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--annotation "data/tiny_dataset/annot/tiny.gff"
-nextflow src/nf_modules/RSEM/quantification_single.nf \
+./nextflow src/nf_modules/RSEM/quantification_single.nf \
-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"
-nextflow src/nf_modules/RSEM/quantification_paired.nf \
+./nextflow src/nf_modules/RSEM/quantification_paired.nf \
-c src/nf_modules/RSEM/quantification_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
diff --git a/src/nf_modules/SAMtools/tests.sh b/src/nf_modules/SAMtools/tests.sh
index 99a7ff32..9b7ac5e4 100755
--- a/src/nf_modules/SAMtools/tests.sh
+++ b/src/nf_modules/SAMtools/tests.sh
@@ -1,19 +1,19 @@
-nextflow src/nf_modules/SAMtools/sort_bams.nf \
+./nextflow src/nf_modules/SAMtools/sort_bams.nf \
-c src/nf_modules/SAMtools/sort_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam"
-nextflow src/nf_modules/SAMtools/index_bams.nf \
+./nextflow src/nf_modules/SAMtools/index_bams.nf \
-c src/nf_modules/SAMtools/index_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.sort.bam"
-nextflow src/nf_modules/SAMtools/split_bams.nf \
+./nextflow src/nf_modules/SAMtools/split_bams.nf \
-c src/nf_modules/SAMtools/split_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam"
-nextflow src/nf_modules/SAMtools/filter_bams.nf \
+./nextflow src/nf_modules/SAMtools/filter_bams.nf \
-c src/nf_modules/SAMtools/filter_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
diff --git a/src/nf_modules/SRAtoolkit/tests.sh b/src/nf_modules/SRAtoolkit/tests.sh
index 526cc7c2..d8575eb4 100755
--- a/src/nf_modules/SRAtoolkit/tests.sh
+++ b/src/nf_modules/SRAtoolkit/tests.sh
@@ -1,4 +1,4 @@
-nextflow src/nf_modules/SRAtoolkit/fastqdump.nf \
+./nextflow src/nf_modules/SRAtoolkit/fastqdump.nf \
-c src/nf_modules/SRAtoolkit/fastqdump.config \
-profile docker \
--list_srr "src/nf_modules/SRAtoolkit/list-srr.txt"
diff --git a/src/nf_modules/UrQt/tests.sh b/src/nf_modules/UrQt/tests.sh
index 436e9cbd..96f58453 100755
--- a/src/nf_modules/UrQt/tests.sh
+++ b/src/nf_modules/UrQt/tests.sh
@@ -1,9 +1,9 @@
-nextflow src/nf_modules/UrQt/trimming_paired.nf \
+./nextflow src/nf_modules/UrQt/trimming_paired.nf \
-c src/nf_modules/UrQt/trimming_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/UrQt/trimming_single.nf \
+./nextflow src/nf_modules/UrQt/trimming_single.nf \
-c src/nf_modules/UrQt/trimming_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
diff --git a/src/nf_modules/cutadapt/tests.sh b/src/nf_modules/cutadapt/tests.sh
index cf2b529e..75089624 100755
--- a/src/nf_modules/cutadapt/tests.sh
+++ b/src/nf_modules/cutadapt/tests.sh
@@ -1,19 +1,19 @@
-nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
+./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
-c src/nf_modules/cutadapt/adaptor_removal_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
+./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
-c src/nf_modules/cutadapt/adaptor_removal_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-nextflow src/nf_modules/cutadapt/trimming_paired.nf \
+./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
-c src/nf_modules/cutadapt/trimming_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/cutadapt/trimming_single.nf \
+./nextflow src/nf_modules/cutadapt/trimming_single.nf \
-c src/nf_modules/cutadapt/trimming_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
--
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