From 2150d981381435d302da8ccce1fc8b9b2105c0ab Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 4 Jun 2021 09:25:15 +0200
Subject: [PATCH] cleanup DSL1 test.sh

---
 src/nf_modules/bedtools/tests.sh   | 15 ---------
 src/nf_modules/bowtie/tests.sh     | 41 ------------------------
 src/nf_modules/bowtie2/tests.sh    | 41 ------------------------
 src/nf_modules/bwa/tests.sh        | 42 ------------------------
 src/nf_modules/cutadapt/tests.sh   | 49 ----------------------------
 src/nf_modules/deeptools/tests.sh  | 46 ---------------------------
 src/nf_modules/fastp/tests.sh      | 25 ---------------
 src/nf_modules/fastqc/tests.sh     | 25 ---------------
 src/nf_modules/hisat2/tests.sh     | 39 -----------------------
 src/nf_modules/htseq/tests.sh      | 15 ---------
 src/nf_modules/kallisto/tests.sh   | 41 ------------------------
 src/nf_modules/macs2/tests.sh      | 18 -----------
 src/nf_modules/multiqc/tests.sh    | 25 ---------------
 src/nf_modules/music/tests.sh      | 20 ------------
 src/nf_modules/rsem/tests.sh       | 44 --------------------------
 src/nf_modules/sambamba/tests.sh   | 37 ----------------------
 src/nf_modules/samblaster/tests.sh | 13 --------
 src/nf_modules/samtools/tests.sh   | 51 ------------------------------
 src/nf_modules/sratoolkit/tests.sh | 13 --------
 src/nf_modules/star/tests.sh       | 43 -------------------------
 src/nf_modules/subread/tests.sh    | 15 ---------
 src/nf_modules/urqt/tests.sh       | 25 ---------------
 22 files changed, 683 deletions(-)
 delete mode 100755 src/nf_modules/bedtools/tests.sh
 delete mode 100755 src/nf_modules/bowtie/tests.sh
 delete mode 100755 src/nf_modules/bowtie2/tests.sh
 delete mode 100755 src/nf_modules/bwa/tests.sh
 delete mode 100755 src/nf_modules/cutadapt/tests.sh
 delete mode 100755 src/nf_modules/deeptools/tests.sh
 delete mode 100755 src/nf_modules/fastp/tests.sh
 delete mode 100755 src/nf_modules/fastqc/tests.sh
 delete mode 100755 src/nf_modules/hisat2/tests.sh
 delete mode 100755 src/nf_modules/htseq/tests.sh
 delete mode 100755 src/nf_modules/kallisto/tests.sh
 delete mode 100755 src/nf_modules/macs2/tests.sh
 delete mode 100755 src/nf_modules/multiqc/tests.sh
 delete mode 100755 src/nf_modules/music/tests.sh
 delete mode 100755 src/nf_modules/rsem/tests.sh
 delete mode 100755 src/nf_modules/sambamba/tests.sh
 delete mode 100755 src/nf_modules/samblaster/tests.sh
 delete mode 100755 src/nf_modules/samtools/tests.sh
 delete mode 100755 src/nf_modules/sratoolkit/tests.sh
 delete mode 100755 src/nf_modules/star/tests.sh
 delete mode 100755 src/nf_modules/subread/tests.sh
 delete mode 100755 src/nf_modules/urqt/tests.sh

diff --git a/src/nf_modules/bedtools/tests.sh b/src/nf_modules/bedtools/tests.sh
deleted file mode 100755
index 61b3cc9c..00000000
--- a/src/nf_modules/bedtools/tests.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-./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" \
-  --bed "data/tiny_dataset/annot/tiny.bed" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/bedtools/fasta_from_bed.nf \
-  -c src/nf_modules/bedtools/fasta_from_bed.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --bed "data/tiny_dataset/annot/tiny.bed" \
-  -resume
-fi
diff --git a/src/nf_modules/bowtie/tests.sh b/src/nf_modules/bowtie/tests.sh
deleted file mode 100755
index a3052918..00000000
--- a/src/nf_modules/bowtie/tests.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-./nextflow src/nf_modules/bowtie/indexing.nf \
-  -c src/nf_modules/bowtie/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/bowtie/mapping_single.nf \
-  -c src/nf_modules/bowtie/mapping_single.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/bowtie/mapping_paired.nf \
-  -c src/nf_modules/bowtie/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/bowtie/indexing.nf \
-  -c src/nf_modules/bowtie/indexing.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/bowtie/mapping_single.nf \
-  -c src/nf_modules/bowtie/mapping_single.config \
-  -profile singularity \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/bowtie/mapping_paired.nf \
-  -c src/nf_modules/bowtie/mapping_paired.config \
-  -profile singularity \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/bowtie2/tests.sh b/src/nf_modules/bowtie2/tests.sh
deleted file mode 100755
index bfec0d53..00000000
--- a/src/nf_modules/bowtie2/tests.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-./nextflow src/nf_modules/bowtie2/indexing.nf \
-  -c src/nf_modules/bowtie2/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/bowtie2/mapping_single.nf \
-  -c src/nf_modules/bowtie2/mapping_single.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/bowtie2/mapping_paired.nf \
-  -c src/nf_modules/bowtie2/mapping_paired.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/bowtie2/indexing.nf \
-  -c src/nf_modules/bowtie2/indexing.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/bowtie2/mapping_single.nf \
-  -c src/nf_modules/bowtie2/mapping_single.config \
-  -profile singularity \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/bowtie2/mapping_paired.nf \
-  -c src/nf_modules/bowtie2/mapping_paired.config \
-  -profile singularity \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/bwa/tests.sh b/src/nf_modules/bwa/tests.sh
deleted file mode 100755
index e601d200..00000000
--- a/src/nf_modules/bwa/tests.sh
+++ /dev/null
@@ -1,42 +0,0 @@
-./nextflow src/nf_modules/bwa/indexing.nf \
-  -c src/nf_modules/bwa/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-# ./nextflow src/nf_modules/bwa/mapping_single.nf \
-#   -c src/nf_modules/bwa/mapping_single.config \
-#   -profile docker \
-#   --index "results/mapping/index/tiny_v2.index" \
-#   --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/bwa/mapping_paired.nf \
-  -c src/nf_modules/bwa/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/bwa/indexing.nf \
-  -c src/nf_modules/bwa/indexing.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-
-# ./nextflow src/nf_modules/bwa/mapping_single.nf \
-#   -c src/nf_modules/bwa/mapping_single.config \
-#   -profile singularity \
-#   --index "results/mapping/index/tiny_v2.index" \
-#   --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/bwa/mapping_paired.nf \
-  -c src/nf_modules/bwa/mapping_paired.config \
-  -profile singularity \
-  --index "results/mapping/index/tiny_v2.*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-fi
diff --git a/src/nf_modules/cutadapt/tests.sh b/src/nf_modules/cutadapt/tests.sh
deleted file mode 100755
index 77712b20..00000000
--- a/src/nf_modules/cutadapt/tests.sh
+++ /dev/null
@@ -1,49 +0,0 @@
-./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" \
-  -resume
-
-./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" \
-  -resume
-
-./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" \
-  -resume
-
-./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" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
-  -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
-  -c src/nf_modules/cutadapt/adaptor_removal_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
-  -c src/nf_modules/cutadapt/trimming_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/cutadapt/trimming_single.nf \
-  -c src/nf_modules/cutadapt/trimming_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
deleted file mode 100755
index 4253689a..00000000
--- a/src/nf_modules/deeptools/tests.sh
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/bin/sh
-
-cp data/tiny_dataset/map/tiny_v2.sort.bam \
-  data/tiny_dataset/map/tiny_v2_bis.sort.bam
-
-./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
-  -c src/nf_modules/deeptools/bam_to_bigwig.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
-  -resume
-
-./nextflow src/nf_modules/deeptools/compute_matrix.nf \
-  -c src/nf_modules/deeptools/compute_matrix.config \
-  -profile docker \
-  --bw "results/mapping/bigwig/*.bw" \
-  --bed "data/tiny_dataset/annot/tiny.bed" \
-  -resume
-
-./nextflow src/nf_modules/deeptools/plot_profile.nf \
-  -c src/nf_modules/deeptools/plot_profile.config \
-  -profile docker \
-  --matrix "results/mapping/region_matrix/*.mat.gz" \
-  --title "plot title" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
-  -c src/nf_modules/deeptools/bam_to_bigwig.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
-  -resume
-
-./nextflow src/nf_modules/deeptools/compute_matrix.nf \
-  -c src/nf_modules/deeptools/compute_matrix.config \
-  -profile docker \
-  --bw "results/mapping/bigwig/*.bw" \
-  --bed "data/tiny_dataset/annot/tiny.bed" \
-  -resume
-
-./nextflow src/nf_modules/deeptools/plot_profile.nf \
-  -c src/nf_modules/deeptools/plot_profile.config \
-  -profile docker \
-  --matrix "results/mapping/region_matrix/*.mat.gz" \
-  --title "plot title" \
-  -resume
-fi
diff --git a/src/nf_modules/fastp/tests.sh b/src/nf_modules/fastp/tests.sh
deleted file mode 100755
index fae4f08a..00000000
--- a/src/nf_modules/fastp/tests.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-./nextflow src/nf_modules/fastp/fastp_paired.nf \
-  -c src/nf_modules/fastp/fastp_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/fastp/fastp_single.nf \
-  -c src/nf_modules/fastp/fastp_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/fastp/fastp_paired.nf \
-  -c src/nf_modules/fastp/fastp_paired.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/fastp/fastp_single.nf \
-  -c src/nf_modules/fastp/fastp_single.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/fastqc/tests.sh b/src/nf_modules/fastqc/tests.sh
deleted file mode 100755
index 7002e71d..00000000
--- a/src/nf_modules/fastqc/tests.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
-  -c src/nf_modules/fastqc/fastqc_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/fastqc/fastqc_single.nf \
-  -c src/nf_modules/fastqc/fastqc_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
-  -c src/nf_modules/fastqc/fastqc_paired.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/fastqc/fastqc_single.nf \
-  -c src/nf_modules/fastqc/fastqc_single.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/hisat2/tests.sh b/src/nf_modules/hisat2/tests.sh
deleted file mode 100755
index 50e43966..00000000
--- a/src/nf_modules/hisat2/tests.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-./nextflow src/nf_modules/hisat2/indexing.nf \
-  -c src/nf_modules/hisat2/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/hisat2/mapping_paired.nf \
-  -c src/nf_modules/hisat2/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/hisat2/mapping_single.nf \
-  -c src/nf_modules/hisat2/mapping_single.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/hisat2/indexing.nf \
-  -c src/nf_modules/hisat2/indexing.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/hisat2/mapping_paired.nf \
-  -c src/nf_modules/hisat2/mapping_paired.config \
-  -profile singularity \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-
-./nextflow src/nf_modules/hisat2/mapping_single.nf \
-  -c src/nf_modules/hisat2/mapping_single.config \
-  -profile singularity \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-fi
diff --git a/src/nf_modules/htseq/tests.sh b/src/nf_modules/htseq/tests.sh
deleted file mode 100755
index eada26b6..00000000
--- a/src/nf_modules/htseq/tests.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-./nextflow src/nf_modules/htseq/htseq.nf \
-  -c src/nf_modules/htseq/htseq.config \
-  -profile docker \
-  --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/htseq/htseq.nf \
-  -c src/nf_modules/htseq/htseq.config \
-  -profile singularity \
-  --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-fi
diff --git a/src/nf_modules/kallisto/tests.sh b/src/nf_modules/kallisto/tests.sh
deleted file mode 100755
index 412a2975..00000000
--- a/src/nf_modules/kallisto/tests.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-./nextflow src/nf_modules/kallisto/indexing.nf \
-  -c src/nf_modules/kallisto/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/kallisto/mapping_single.nf \
-  -c src/nf_modules/kallisto/mapping_single.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/kallisto/mapping_paired.nf \
-  -c src/nf_modules/kallisto/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/kallisto/indexing.nf \
-  -c src/nf_modules/kallisto/indexing.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  -resume
-
-./nextflow src/nf_modules/kallisto/mapping_single.nf \
-  -c src/nf_modules/kallisto/mapping_single.config \
-  -profile singularity \
-  --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/kallisto/mapping_paired.nf \
-  -c src/nf_modules/kallisto/mapping_paired.config \
-  -profile singularity \
-  --index "results/mapping/index/tiny_v2.index" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/macs2/tests.sh b/src/nf_modules/macs2/tests.sh
deleted file mode 100755
index fc73ce29..00000000
--- a/src/nf_modules/macs2/tests.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-cp data/tiny_dataset/map/tiny_v2.bam data/tiny_dataset/map/tiny_v2_control.bam
-./nextflow src/nf_modules/macs2/peak_calling.nf \
-  -c src/nf_modules/macs2/peak_calling.config \
-  -profile docker \
-  -resume \
-  --bam "data/tiny_dataset/map/tiny_v2*.bam" \
-  --genome_size 129984 \
-  --control_tag "control"
-
-if [ -x "$(command -v singularity)" ]; then
-  ./nextflow src/nf_modules/macs2/peak_calling.nf \
-    -c src/nf_modules/macs2/peak_calling.config \
-    -profile singularity \
-    -resume \
-    --bam "data/tiny_dataset/map/tiny_v2*.bam" \
-    --genome_size 129984 \
-    --control_tag "control"
-fi
diff --git a/src/nf_modules/multiqc/tests.sh b/src/nf_modules/multiqc/tests.sh
deleted file mode 100755
index ff23852b..00000000
--- a/src/nf_modules/multiqc/tests.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-./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" \
-  -resume
-
-./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" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
-  -c src/nf_modules/multiqc/multiqc_paired.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/multiqc/multiqc_single.nf \
-  -c src/nf_modules/multiqc/multiqc_single.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/music/tests.sh b/src/nf_modules/music/tests.sh
deleted file mode 100755
index 4169c449..00000000
--- a/src/nf_modules/music/tests.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_control.sort.bam
-./nextflow src/nf_modules/music/peak_calling_single.nf \
-  -c src/nf_modules/music/peak_calling_single.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --bam "data/tiny_dataset/map/*.sort.bam" \
-  --index "data/tiny_dataset/map/*.sort.bam.bai*" \
-  --read_size 50 --frag_size 300 \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/music/peak_calling_single.nf \
-  -c src/nf_modules/music/peak_calling_single.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --bam "data/tiny_dataset/map/*.sort.bam" \
-  --index "data/tiny_dataset/map/*.sort.bam.bai*" \
-  --read_size 50 --frag_size 300 \
-  -resume
-fi
diff --git a/src/nf_modules/rsem/tests.sh b/src/nf_modules/rsem/tests.sh
deleted file mode 100755
index e4cd2726..00000000
--- a/src/nf_modules/rsem/tests.sh
+++ /dev/null
@@ -1,44 +0,0 @@
-./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" \
-  -resume
-
-./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*_R1.fastq" \
-  -resume
-
-./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*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/rsem/indexing.nf \
-  -c src/nf_modules/rsem/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --annotation "data/tiny_dataset/annot/tiny.gff" \
-  -resume
-
-./nextflow src/nf_modules/rsem/quantification_single.nf \
-  -c src/nf_modules/rsem/quantification_single.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
-  -resume
-
-./nextflow src/nf_modules/rsem/quantification_paired.nf \
-  -c src/nf_modules/rsem/quantification_paired.config \
-  -profile docker \
-  --index "results/mapping/index/tiny_v2.index*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/sambamba/tests.sh b/src/nf_modules/sambamba/tests.sh
deleted file mode 100755
index 256df65f..00000000
--- a/src/nf_modules/sambamba/tests.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-./nextflow src/nf_modules/sambamba/sort_bams.nf \
-  -c src/nf_modules/sambamba/sort_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-./nextflow src/nf_modules/sambamba/index_bams.nf \
-  -c src/nf_modules/sambamba/index_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
-  -resume
-
-./nextflow src/nf_modules/sambamba/split_bams.nf \
-  -c src/nf_modules/sambamba/split_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/sambamba/sort_bams.nf \
-  -c src/nf_modules/sambamba/sort_bams.config \
-  -profile singularity \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-./nextflow src/nf_modules/sambamba/index_bams.nf \
-  -c src/nf_modules/sambamba/index_bams.config \
-  -profile singularity \
-  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
-  -resume
-
-./nextflow src/nf_modules/sambamba/split_bams.nf \
-  -c src/nf_modules/sambamba/split_bams.config \
-  -profile singularity \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-fi
diff --git a/src/nf_modules/samblaster/tests.sh b/src/nf_modules/samblaster/tests.sh
deleted file mode 100755
index 10ad93d7..00000000
--- a/src/nf_modules/samblaster/tests.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-./nextflow src/nf_modules/samblaster/dedup_sams.nf \
-  -c src/nf_modules/samblaster/dedup_sams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/samblaster/dedup_sams.nf \
-  -c src/nf_modules/samblaster/dedup_sams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-fi
diff --git a/src/nf_modules/samtools/tests.sh b/src/nf_modules/samtools/tests.sh
deleted file mode 100755
index 256fa058..00000000
--- a/src/nf_modules/samtools/tests.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-./nextflow src/nf_modules/samtools/sort_bams.nf \
-  -c src/nf_modules/samtools/sort_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-./nextflow src/nf_modules/samtools/index_bams.nf \
-  -c src/nf_modules/samtools/index_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
-  -resume
-
-./nextflow src/nf_modules/samtools/split_bams.nf \
-  -c src/nf_modules/samtools/split_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-./nextflow src/nf_modules/samtools/filter_bams.nf \
-  -c src/nf_modules/samtools/filter_bams.config \
-  -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  --bed "data/tiny_dataset/OLD/2genes.bed" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./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" \
-  -resume
-
-./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" \
-  -resume
-
-./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" \
-  -resume
-
-./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" \
-  --bed "data/tiny_dataset/OLD/2genes.bed" \
-  -resume
-fi
diff --git a/src/nf_modules/sratoolkit/tests.sh b/src/nf_modules/sratoolkit/tests.sh
deleted file mode 100755
index 1747137d..00000000
--- a/src/nf_modules/sratoolkit/tests.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-./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" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/sratoolkit/fastqdump.nf \
-  -c src/nf_modules/sratoolkit/fastqdump.config \
-  -profile docker \
-  --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
-  -resume
-fi
diff --git a/src/nf_modules/star/tests.sh b/src/nf_modules/star/tests.sh
deleted file mode 100755
index 046ffe4f..00000000
--- a/src/nf_modules/star/tests.sh
+++ /dev/null
@@ -1,43 +0,0 @@
-./nextflow src/nf_modules/star/indexing.nf \
-  -c src/nf_modules/star/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --annotation "data/tiny_dataset/annot/tiny.gtf" \
-  -resume
-
-./nextflow src/nf_modules/star/mapping_single.nf \
-  -c src/nf_modules/star/mapping_single.config \
-  -profile docker \
-  --index "results/mapping/index/*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/star/mapping_paired.nf \
-  -c src/nf_modules/star/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/star/indexing.nf \
-  -c src/nf_modules/star/indexing.config \
-  -profile singularity \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --annotation "data/tiny_dataset/annot/tiny.gtf" \
-  -resume
-
-./nextflow src/nf_modules/star/mapping_single.nf \
-  -c src/nf_modules/star/mapping_single.config \
-  -profile singularity \
-  --index "results/mapping/index/*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-  -resume
-
-./nextflow src/nf_modules/star/mapping_paired.nf \
-  -c src/nf_modules/star/mapping_paired.config \
-  -profile singularity \
-  --index "results/mapping/index/*" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-  -resume
-fi
diff --git a/src/nf_modules/subread/tests.sh b/src/nf_modules/subread/tests.sh
deleted file mode 100755
index c50b20e3..00000000
--- a/src/nf_modules/subread/tests.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-./nextflow src/nf_modules/subread/subread.nf \
-  -c src/nf_modules/subread/subread.config \
-  -profile docker \
-  --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/subread/subread.nf \
-  -c src/nf_modules/subread/subread.config \
-  -profile singularity \
-  --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam" \
-  -resume
-fi
diff --git a/src/nf_modules/urqt/tests.sh b/src/nf_modules/urqt/tests.sh
deleted file mode 100755
index 9992c674..00000000
--- a/src/nf_modules/urqt/tests.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-./nextflow src/nf_modules/urqt/trimming_paired.nf \
-  -c src/nf_modules/urqt/trimming_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/urqt/trimming_single.nf \
-  -c src/nf_modules/urqt/trimming_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/urqt/trimming_single.nf \
-  -c src/nf_modules/urqt/trimming_single.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-
-./nextflow src/nf_modules/urqt/trimming_single.nf \
-  -c src/nf_modules/urqt/trimming_single.config \
-  -profile singularity \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-  -resume
-fi
-- 
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