diff --git a/src/nf_modules/bedtools/tests.sh b/src/nf_modules/bedtools/tests.sh
deleted file mode 100755
index 61b3cc9c44bad7f171e87f180f2a2a156009d48f..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/bedtools/fasta_from_bed.nf \
- -c src/nf_modules/bedtools/fasta_from_bed.config \
- -profile singularity \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- --bed "data/tiny_dataset/annot/tiny.bed" \
- -resume
-fi
diff --git a/src/nf_modules/bowtie/tests.sh b/src/nf_modules/bowtie/tests.sh
deleted file mode 100755
index a30529182addf06c272ca86f9d438d0647b0f49e..0000000000000000000000000000000000000000
--- a/src/nf_modules/bowtie/tests.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-./nextflow src/nf_modules/bowtie/indexing.nf \
- -c src/nf_modules/bowtie/indexing.config \
- -profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- -resume
-
-./nextflow src/nf_modules/bowtie/mapping_single.nf \
- -c src/nf_modules/bowtie/mapping_single.config \
- -profile docker \
- --index "results/mapping/index/*.ebwt" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
- -resume
-
-./nextflow src/nf_modules/bowtie/mapping_paired.nf \
- -c src/nf_modules/bowtie/mapping_paired.config \
- -profile docker \
- --index "results/mapping/index/*.ebwt" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
- -resume
-
-if [ -x "$(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 bfec0d533a6430fb6cac928fe7350f3fa97a01ae..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/bowtie2/indexing.nf \
- -c src/nf_modules/bowtie2/indexing.config \
- -profile singularity \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- -resume
-
-./nextflow src/nf_modules/bowtie2/mapping_single.nf \
- -c src/nf_modules/bowtie2/mapping_single.config \
- -profile singularity \
- --index "data/tiny_dataset/fasta/*.bt2" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
- -resume
-
-./nextflow src/nf_modules/bowtie2/mapping_paired.nf \
- -c src/nf_modules/bowtie2/mapping_paired.config \
- -profile singularity \
- --index "data/tiny_dataset/fasta/*.bt2" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
- -resume
-fi
diff --git a/src/nf_modules/bwa/tests.sh b/src/nf_modules/bwa/tests.sh
deleted file mode 100755
index e601d200cd9b642ad7d96ff05be666938e2c6178..0000000000000000000000000000000000000000
--- a/src/nf_modules/bwa/tests.sh
+++ /dev/null
@@ -1,42 +0,0 @@
-./nextflow src/nf_modules/bwa/indexing.nf \
- -c src/nf_modules/bwa/indexing.config \
- -profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- -resume
-
-# ./nextflow src/nf_modules/bwa/mapping_single.nf \
-# -c src/nf_modules/bwa/mapping_single.config \
-# -profile docker \
-# --index "results/mapping/index/tiny_v2.index" \
-# --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/bwa/mapping_paired.nf \
- -c src/nf_modules/bwa/mapping_paired.config \
- -profile docker \
- --index "results/mapping/index/tiny_v2.*" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
- -resume
-
-
-if [ -x "$(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 77712b2083e0ba335a3f0c1944c2e8045b66f4c7..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
- -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
- -resume
-
-./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
- -c src/nf_modules/cutadapt/adaptor_removal_single.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
- -resume
-
-./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
- -c src/nf_modules/cutadapt/trimming_paired.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
- -resume
-
-./nextflow src/nf_modules/cutadapt/trimming_single.nf \
- -c src/nf_modules/cutadapt/trimming_single.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
- -resume
-fi
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
deleted file mode 100755
index 4253689a7c94a62feec6be1536f11d394fec909b..0000000000000000000000000000000000000000
--- a/src/nf_modules/deeptools/tests.sh
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/bin/sh
-
-cp data/tiny_dataset/map/tiny_v2.sort.bam \
- data/tiny_dataset/map/tiny_v2_bis.sort.bam
-
-./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
- -c src/nf_modules/deeptools/bam_to_bigwig.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
- -resume
-
-./nextflow src/nf_modules/deeptools/compute_matrix.nf \
- -c src/nf_modules/deeptools/compute_matrix.config \
- -profile docker \
- --bw "results/mapping/bigwig/*.bw" \
- --bed "data/tiny_dataset/annot/tiny.bed" \
- -resume
-
-./nextflow src/nf_modules/deeptools/plot_profile.nf \
- -c src/nf_modules/deeptools/plot_profile.config \
- -profile docker \
- --matrix "results/mapping/region_matrix/*.mat.gz" \
- --title "plot title" \
- -resume
-
-if [ -x "$(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 fae4f08a92c56752b4d467b5c31aca629eb2aac3..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/fastp/fastp_paired.nf \
- -c src/nf_modules/fastp/fastp_paired.config \
- -profile singularity \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
- -resume
-
-./nextflow src/nf_modules/fastp/fastp_single.nf \
- -c src/nf_modules/fastp/fastp_single.config \
- -profile singularity \
- --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
- -resume
-fi
diff --git a/src/nf_modules/fastqc/tests.sh b/src/nf_modules/fastqc/tests.sh
deleted file mode 100755
index 7002e71d6396d407f5ba9f37864ccdbf661597f3..0000000000000000000000000000000000000000
--- a/src/nf_modules/fastqc/tests.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
- -c src/nf_modules/fastqc/fastqc_paired.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
- -resume
-
-./nextflow src/nf_modules/fastqc/fastqc_single.nf \
- -c src/nf_modules/fastqc/fastqc_single.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
- -resume
-
-if [ -x "$(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 50e4396652e867a3bc114db2ba79b4af4dc7de9a..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/hisat2/indexing.nf \
- -c src/nf_modules/hisat2/indexing.config \
- -profile singularity \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- -resume
-
-./nextflow src/nf_modules/hisat2/mapping_paired.nf \
- -c src/nf_modules/hisat2/mapping_paired.config \
- -profile singularity \
- --index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-
-./nextflow src/nf_modules/hisat2/mapping_single.nf \
- -c src/nf_modules/hisat2/mapping_single.config \
- -profile singularity \
- --index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-fi
diff --git a/src/nf_modules/htseq/tests.sh b/src/nf_modules/htseq/tests.sh
deleted file mode 100755
index eada26b6d280b80f6ebb7db3d3dc5bf652013b27..0000000000000000000000000000000000000000
--- a/src/nf_modules/htseq/tests.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-./nextflow src/nf_modules/htseq/htseq.nf \
- -c src/nf_modules/htseq/htseq.config \
- -profile docker \
- --gtf "data/tiny_dataset/annot/tiny.gff" \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- -resume
-
-if [ -x "$(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 412a29754d7948ba562b31e7b54038db80f60241..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/kallisto/indexing.nf \
- -c src/nf_modules/kallisto/indexing.config \
- -profile singularity \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- -resume
-
-./nextflow src/nf_modules/kallisto/mapping_single.nf \
- -c src/nf_modules/kallisto/mapping_single.config \
- -profile singularity \
- --index "results/mapping/index/tiny_v2.index" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
- -resume
-
-./nextflow src/nf_modules/kallisto/mapping_paired.nf \
- -c src/nf_modules/kallisto/mapping_paired.config \
- -profile singularity \
- --index "results/mapping/index/tiny_v2.index" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
- -resume
-fi
diff --git a/src/nf_modules/macs2/tests.sh b/src/nf_modules/macs2/tests.sh
deleted file mode 100755
index fc73ce29a9e9aed5ee83ba0e171e49059185bc5c..0000000000000000000000000000000000000000
--- a/src/nf_modules/macs2/tests.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-cp data/tiny_dataset/map/tiny_v2.bam data/tiny_dataset/map/tiny_v2_control.bam
-./nextflow src/nf_modules/macs2/peak_calling.nf \
- -c src/nf_modules/macs2/peak_calling.config \
- -profile docker \
- -resume \
- --bam "data/tiny_dataset/map/tiny_v2*.bam" \
- --genome_size 129984 \
- --control_tag "control"
-
-if [ -x "$(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 ff23852be9e17167a860752f869a5cde154e4d87..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
- -c src/nf_modules/multiqc/multiqc_paired.config \
- -profile singularity \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
- -resume
-
-./nextflow src/nf_modules/multiqc/multiqc_single.nf \
- -c src/nf_modules/multiqc/multiqc_single.config \
- -profile singularity \
- --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
- -resume
-fi
diff --git a/src/nf_modules/music/tests.sh b/src/nf_modules/music/tests.sh
deleted file mode 100755
index 4169c449d5706e01a28c443247bf04c2a39fe40d..0000000000000000000000000000000000000000
--- a/src/nf_modules/music/tests.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_control.sort.bam
-./nextflow src/nf_modules/music/peak_calling_single.nf \
- -c src/nf_modules/music/peak_calling_single.config \
- -profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- --bam "data/tiny_dataset/map/*.sort.bam" \
- --index "data/tiny_dataset/map/*.sort.bam.bai*" \
- --read_size 50 --frag_size 300 \
- -resume
-
-if [ -x "$(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 e4cd27267371e378d4c47454f9344298cdde4566..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/rsem/indexing.nf \
- -c src/nf_modules/rsem/indexing.config \
- -profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- --annotation "data/tiny_dataset/annot/tiny.gff" \
- -resume
-
-./nextflow src/nf_modules/rsem/quantification_single.nf \
- -c src/nf_modules/rsem/quantification_single.config \
- -profile docker \
- --index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
- -resume
-
-./nextflow src/nf_modules/rsem/quantification_paired.nf \
- -c src/nf_modules/rsem/quantification_paired.config \
- -profile docker \
- --index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
- -resume
-fi
diff --git a/src/nf_modules/sambamba/tests.sh b/src/nf_modules/sambamba/tests.sh
deleted file mode 100755
index 256df65f9ed23efac640aea6548f15397479ca60..0000000000000000000000000000000000000000
--- a/src/nf_modules/sambamba/tests.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-./nextflow src/nf_modules/sambamba/sort_bams.nf \
- -c src/nf_modules/sambamba/sort_bams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- -resume
-
-./nextflow src/nf_modules/sambamba/index_bams.nf \
- -c src/nf_modules/sambamba/index_bams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
- -resume
-
-./nextflow src/nf_modules/sambamba/split_bams.nf \
- -c src/nf_modules/sambamba/split_bams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- -resume
-
-if [ -x "$(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 10ad93d7841ba4b708664803c0ca1299cc34ee19..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/samblaster/dedup_sams.nf \
- -c src/nf_modules/samblaster/dedup_sams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- -resume
-fi
diff --git a/src/nf_modules/samtools/tests.sh b/src/nf_modules/samtools/tests.sh
deleted file mode 100755
index 256fa058beeaf3464391f4e974a2b4a2ef499b0c..0000000000000000000000000000000000000000
--- a/src/nf_modules/samtools/tests.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-./nextflow src/nf_modules/samtools/sort_bams.nf \
- -c src/nf_modules/samtools/sort_bams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- -resume
-
-./nextflow src/nf_modules/samtools/index_bams.nf \
- -c src/nf_modules/samtools/index_bams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
- -resume
-
-./nextflow src/nf_modules/samtools/split_bams.nf \
- -c src/nf_modules/samtools/split_bams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- -resume
-
-./nextflow src/nf_modules/samtools/filter_bams.nf \
- -c src/nf_modules/samtools/filter_bams.config \
- -profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- --bed "data/tiny_dataset/OLD/2genes.bed" \
- -resume
-
-if [ -x "$(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 1747137d454630bffa8538efc3009469f271b50c..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/sratoolkit/fastqdump.nf \
- -c src/nf_modules/sratoolkit/fastqdump.config \
- -profile docker \
- --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
- -resume
-fi
diff --git a/src/nf_modules/star/tests.sh b/src/nf_modules/star/tests.sh
deleted file mode 100755
index 046ffe4f32bc78467a61440774553335f888b288..0000000000000000000000000000000000000000
--- a/src/nf_modules/star/tests.sh
+++ /dev/null
@@ -1,43 +0,0 @@
-./nextflow src/nf_modules/star/indexing.nf \
- -c src/nf_modules/star/indexing.config \
- -profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- --annotation "data/tiny_dataset/annot/tiny.gtf" \
- -resume
-
-./nextflow src/nf_modules/star/mapping_single.nf \
- -c src/nf_modules/star/mapping_single.config \
- -profile docker \
- --index "results/mapping/index/*" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
- -resume
-
-./nextflow src/nf_modules/star/mapping_paired.nf \
- -c src/nf_modules/star/mapping_paired.config \
- -profile docker \
- --index "results/mapping/index/*" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
- -resume
-
-if [ -x "$(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 c50b20e3601efeaa8a0d3721ad6ab20739c3db48..0000000000000000000000000000000000000000
--- 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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/subread/subread.nf \
- -c src/nf_modules/subread/subread.config \
- -profile singularity \
- --gtf "data/tiny_dataset/annot/tiny.gff" \
- --bam "data/tiny_dataset/map/tiny_v2.bam" \
- -resume
-fi
diff --git a/src/nf_modules/urqt/tests.sh b/src/nf_modules/urqt/tests.sh
deleted file mode 100755
index 9992c67490ce65df42471a73d5c36bb0b708763e..0000000000000000000000000000000000000000
--- a/src/nf_modules/urqt/tests.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-./nextflow src/nf_modules/urqt/trimming_paired.nf \
- -c src/nf_modules/urqt/trimming_paired.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
- -resume
-
-./nextflow src/nf_modules/urqt/trimming_single.nf \
- -c src/nf_modules/urqt/trimming_single.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
- -resume
-
-if [ -x "$(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