From 9b037d38ac31b76ece50ed0c93b73d19dabb789d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Mar 2019 11:11:44 +0100
Subject: [PATCH] update link for all modules names to lowercase
---
README.md | 2 +-
doc/TP_computational_biologists.md | 32 +++++++++----------
doc/TP_experimental_biologists.md | 18 +++++------
.../bedtools/2.25.0/docker_init.sh | 2 +-
.../bowtie/1.2.2/docker_init.sh | 2 +-
.../bowtie2/2.3.4.1/docker_init.sh | 2 +-
src/docker_modules/bwa/0.7.17/docker_init.sh | 2 +-
.../deeptools/3.0.2/docker_init.sh | 2 +-
.../deeptools/3.1.1/docker_init.sh | 2 +-
.../fastqc/0.11.5/docker_init.sh | 2 +-
.../gatk/4.0.8.1/docker_init.sh | 2 +-
.../hisat2/2.0.0/docker_init.sh | 2 +-
src/docker_modules/htseq/0.8.0/docker_init.sh | 2 +-
.../kallisto/0.43.1/docker_init.sh | 2 +-
.../kallisto/0.44.0/docker_init.sh | 2 +-
src/docker_modules/macs2/2.1.0/docker_init.sh | 2 +-
src/docker_modules/multiqc/1.0/docker_init.sh | 2 +-
.../music/6613c53/docker_init.sh | 2 +-
src/docker_modules/rsem/1.3.0/docker_init.sh | 2 +-
.../salmon/0.8.2/docker_init.sh | 2 +-
.../samtools/1.7/docker_init.sh | 2 +-
.../sratoolkit/2.8.2/docker_init.sh | 2 +-
.../tophat/2.1.1/docker_init.sh | 2 +-
.../trimmomatic/0.36/docker_init.sh | 2 +-
.../urqt/d62c1f8/docker_init.sh | 2 +-
src/nf_modules/bedtools/tests.sh | 8 ++---
src/nf_modules/bowtie/tests.sh | 24 +++++++-------
src/nf_modules/bowtie2/tests.sh | 24 +++++++-------
src/nf_modules/bwa/tests.sh | 24 +++++++-------
src/nf_modules/deeptools/tests.sh | 6 ++--
src/nf_modules/fastqc/tests.sh | 8 ++---
src/nf_modules/htseq/tests.sh | 4 +--
src/nf_modules/kallisto/tests.sh | 12 +++----
src/nf_modules/multiqc/tests.sh | 8 ++---
src/nf_modules/music/tests.sh | 4 +--
src/nf_modules/rsem/tests.sh | 12 +++----
src/nf_modules/samtools/tests.sh | 16 +++++-----
src/nf_modules/sratoolkit/tests.sh | 6 ++--
src/nf_modules/urqt/tests.sh | 16 +++++-----
src/singularity_modules/UrQt/d62c1f8/build.sh | 3 --
.../bedtools/2.25.0/build.sh | 2 +-
src/singularity_modules/bowtie/1.2.2/build.sh | 2 +-
.../bowtie2/2.3.4.1/build.sh | 2 +-
src/singularity_modules/bwa/0.7.17/build.sh | 2 +-
.../{UrQt => urqt}/d62c1f8/UrQt.def | 0
src/singularity_modules/urqt/d62c1f8/build.sh | 3 ++
46 files changed, 141 insertions(+), 141 deletions(-)
delete mode 100755 src/singularity_modules/UrQt/d62c1f8/build.sh
rename src/singularity_modules/{UrQt => urqt}/d62c1f8/UrQt.def (100%)
create mode 100755 src/singularity_modules/urqt/d62c1f8/build.sh
diff --git a/README.md b/README.md
index c83d221d..99142730 100644
--- a/README.md
+++ b/README.md
@@ -73,7 +73,7 @@ src/nf_modules/<tool_name>/<tool_version>/tests.sh
For example to run the tests on `Bowtie2` run:
```sh
-src/nf_modules/Bowtie2/tests.sh
+src/nf_modules/bowtie2/tests.sh
```
## Available tools
diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md
index 84138b44..695a16ec 100644
--- a/doc/TP_computational_biologists.md
+++ b/doc/TP_computational_biologists.md
@@ -21,10 +21,10 @@ For the practical you can either work with the WebIDE of Gitlab, or locally as d
To run a tool within a [Docker container](https://www.docker.com/what-container) you need to write a `Dockerfile`.
-[`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) is paired with a [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file like following the example for `Kallisto` version `0.43.1`:
+[`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) is paired with a [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) file like following the example for `Kallisto` version `0.43.1`:
```sh
-$ ls -l src/docker_modules/Kallisto/0.43.1/
+$ ls -l src/docker_modules/kallisto/0.43.1/
total 16K
drwxr-xr-x 2 laurent users 4.0K Jun 5 19:06 ./
drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../
@@ -32,15 +32,15 @@ drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../
-rwxr-xr-x 1 laurent users 79 Jun 5 19:06 docker_init.sh*
```
-## [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh)
-The [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) is a simple sh script with executable rights (`chmod +x`). By executing this script, the user creates a [Docker container](https://www.docker.com/what-container) with the tool installed a specific version. You can check the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file of any implemented tools as a template.
+## [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh)
+The [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) is a simple sh script with executable rights (`chmod +x`). By executing this script, the user creates a [Docker container](https://www.docker.com/what-container) with the tool installed a specific version. You can check the [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) file of any implemented tools as a template.
Remember that the name of the [container](https://www.docker.com/what-container) must be in lower case and in the format `<tool_name>:<version>`.
For tools without a version number you can use a commit hash instead.
-## [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile)
+## [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile)
-The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) file.
+The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) file.
For `Kallisto` version `0.44.0` the header of the `Dockerfile` is :
@@ -57,12 +57,12 @@ Then we declare the *maintainer* of the container. Before declaring an environme
You should always declare a variable `TOOLSNAME_VERSION` that contains the version number of commit number of the tools you wrap. In simple cases you just have to modify this line to create a new `Dockerfile` for another version of the tool.
-The following lines of the [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are a succession of `bash` commands executed as the **root** user within the container.
+The following lines of the [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile) are a succession of `bash` commands executed as the **root** user within the container.
Each `RUN` block is run sequentially by `Docker`. If there is an error or modifications in a `RUN` block, only this block and the following `RUN` will be executed.
You can learn more about the building of Docker containers [here](https://docs.docker.com/engine/reference/builder/#usage).
-When you build your [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile), instead of launching many times the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) script to tests your [container](https://www.docker.com/what-container), you can connect to a base container in interactive mode to launch tests your commands.
+When you build your [`Dockerfile`](./src/docker_modules/kallisto/0.44.0/Dockerfile), instead of launching many times the [`docker_init.sh`](./src/docker_modules/kallisto/0.44.0/docker_init.sh) script to tests your [container](https://www.docker.com/what-container), you can connect to a base container in interactive mode to launch tests your commands.
```sh
docker run -it ubuntu:18.04 bash
@@ -80,8 +80,8 @@ You can read the Contributing guide for the [PMSN/modules](https://gitlab.biolog
The last step to wrap your tool is to make it available in nextflow. For this you need to create at least 4 files, like the following for Kallisto version `0.44.0`:
```sh
-ls -lR src/nf_modules/Kallisto
-src/nf_modules/Kallisto/:
+ls -lR src/nf_modules/kallisto
+src/nf_modules/kallisto/:
total 12
-rw-r--r-- 1 laurent users 551 Jun 18 17:14 index.nf
-rw-r--r-- 1 laurent users 901 Jun 18 17:14 mapping_paired.nf
@@ -89,12 +89,12 @@ total 12
-rwxr-xr-x 1 laurent users 627 Jun 18 17:14 tests.sh*
```
-The [`.config` files](./src/nf_modules/Kallisto/) file contains instructions for two profiles : `psmn` and `docker`.
-The [`.nf` files](./src/nf_modules/Kallisto/) file contains nextflow processes to use `Kallisto`.
+The [`.config` files](./src/nf_modules/kallisto/) file contains instructions for two profiles : `psmn` and `docker`.
+The [`.nf` files](./src/nf_modules/kallisto/) file contains nextflow processes to use `Kallisto`.
-The [`tests/tests.sh`](./src/nf_modules/Kallisto/tests/tests.sh) script (with executable rights), contains a series of nextflow calls on the other `.nf` files of the folder. Those tests correspond to execution of the `*.nf` files present in the [`kallisto folder`](./src/nf_modules/Kallisto/) on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset with the `docker` profile. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md).
+The [`tests/tests.sh`](./src/nf_modules/kallisto/tests/tests.sh) script (with executable rights), contains a series of nextflow calls on the other `.nf` files of the folder. Those tests correspond to execution of the `*.nf` files present in the [`kallisto folder`](./src/nf_modules/kallisto/) on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset with the `docker` profile. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md).
-## [`kallisto.config`](./src/nf_modules/Kallisto/)
+## [`kallisto.config`](./src/nf_modules/kallisto/)
The `.config` file defines the configuration to apply to your process conditionally to the value of the `-profile` option. You must define configuration for at least the `psmn` and `docker` profile.
@@ -160,9 +160,9 @@ process{
The `beforeScript` variable is executed before the main script for the corresponding process.
-## [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf)
+## [`kallisto.nf`](./src/nf_modules/kallisto/kallisto.nf)
-The [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file contains examples of nextflow process that execute Kallisto.
+The [`kallisto.nf`](./src/nf_modules/kallisto/kallisto.nf) file contains examples of nextflow process that execute Kallisto.
- Each example must be usable as it is to be incorporated in a nextflow pipeline.
- You need to define, default value for the parameters passed to the process.
diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index f0aac22e..1a2f3857 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -59,16 +59,16 @@ The `src/docker_modules` contains the code to wrap tools in [Docker](https://www
```sh
ls -l src/docker_modules/
-rwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 BEDtools/
-drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 Bowtie2/
-drwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 FastQC/
-drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 HTSeq/
+rwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 bedtools/
+drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 bowtie2/
+drwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 fastqc/
+drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 htseq/
```
To each `tools/version` corresponds two files:
```sh
-ls -l src/docker_modules/Bowtie2/2.3.4.1/
+ls -l src/docker_modules/bowtie2/2.3.4.1/
-rw-r--r-- 1 laurent _lpoperator 283 Jun 5 15:07 Dockerfile
-rwxr-xr-x 1 laurent _lpoperator 79 Jun 5 16:18 docker_init.sh*
```
@@ -322,7 +322,7 @@ You can test your pipeline with the following command:
The second step of the pipeline is to trim reads by quality.
-Browse for [src/nf_modules/UrQt/trimming_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/UrQt/trimming_paired.nf), this file contains examples for UrQt. We are interested in the *for paired-end data* section of the code. Copy the process section code in your pipeline and commit it.
+Browse for [src/nf_modules/urqt/trimming_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.nf), this file contains examples for UrQt. We are interested in the *for paired-end data* section of the code. Copy the process section code in your pipeline and commit it.
This code won’t work if you try to run it: the `fastq_file` channel is already consumed by the `adaptor_removal` process. In nextflow once a channel is used by a process, it ceases to exist. Moreover, we don’t want to trim the input fastq, we want to trim the fastq that comes from the `adaptor_removal` process.
@@ -340,7 +340,7 @@ set pair_id, file(reads) from fastq_files_cut
The two processes are now connected by the channel `fastq_files_cut`.
-Add the content of the [src/nf_modules/UrQt/trimming_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/UrQt/trimming_paired.config) file to your `src/RNASeq.config` file and commit it.
+Add the content of the [src/nf_modules/urqt/trimming_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.config) file to your `src/RNASeq.config` file and commit it.
You can test your pipeline.
@@ -348,7 +348,7 @@ You can test your pipeline.
Kallisto need the sequences of the transcripts that need to be quantified. We are going to extract these sequences from the reference `data/tiny_dataset/fasta/tiny_v2.fasta` with the `bed` annotation `data/tiny_dataset/annot/tiny.bed`.
-You can copy to your `src/RNASeq.nf` file the content of [src/nf_modules/BEDtools/fasta_from_bed.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/BEDtools/fasta_from_bed.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/BEDtools/fasta_from_bed.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/BEDtools/fasta_from_bed.config).
+You can copy to your `src/RNASeq.nf` file the content of [src/nf_modules/bedtools/fasta_from_bed.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/bedtools/fasta_from_bed.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.config).
Commit your work and test your pipeline with the following command:
@@ -360,7 +360,7 @@ Commit your work and test your pipeline with the following command:
Kallisto run in two steps: the indexation of the reference and the quantification on this index.
-You can copy to your `src/RNASeq.nf` file the content of the files [src/nf_modules/Kallisto/indexing.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/indexing.nf) and [src/nf_modules/Kallisto/mapping_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/mapping_paired.nf). You can add to your file `src/RNASeq.config` file the content of the files [src/nf_modules/Kallisto/indexing.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/indexing.config) and [src/nf_modules/Kallisto/mapping_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/mapping_paired.config).
+You can copy to your `src/RNASeq.nf` file the content of the files [src/nf_modules/kallisto/indexing.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.nf) and [src/nf_modules/kallisto/mapping_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.nf). You can add to your file `src/RNASeq.config` file the content of the files [src/nf_modules/kallisto/indexing.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.config) and [src/nf_modules/kallisto/mapping_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.config).
We are going to work with paired-end so only copy the relevant processes. The `index_fasta` process needs to take as input the output of your `fasta_from_bed` process. The `fastq` input of your `mapping_fastq` process needs to take as input the output of your `index_fasta` process and the `trimming` process.
diff --git a/src/docker_modules/bedtools/2.25.0/docker_init.sh b/src/docker_modules/bedtools/2.25.0/docker_init.sh
index c5c6f802..63da76f2 100755
--- a/src/docker_modules/bedtools/2.25.0/docker_init.sh
+++ b/src/docker_modules/bedtools/2.25.0/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/BEDtools/2.25.0 -t 'bedtools:2.25.0'
+docker build src/docker_modules/bedtools/2.25.0 -t 'bedtools:2.25.0'
diff --git a/src/docker_modules/bowtie/1.2.2/docker_init.sh b/src/docker_modules/bowtie/1.2.2/docker_init.sh
index 8e010a67..c8106dbf 100755
--- a/src/docker_modules/bowtie/1.2.2/docker_init.sh
+++ b/src/docker_modules/bowtie/1.2.2/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/Bowtie/1.2.2 -t 'bowtie:1.2.2'
+docker build src/docker_modules/bowtie/1.2.2 -t 'bowtie:1.2.2'
diff --git a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
index bba04c2b..77141d11 100755
--- a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
+++ b/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/Bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
+docker build src/docker_modules/bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
diff --git a/src/docker_modules/bwa/0.7.17/docker_init.sh b/src/docker_modules/bwa/0.7.17/docker_init.sh
index 888bec68..d2031220 100755
--- a/src/docker_modules/bwa/0.7.17/docker_init.sh
+++ b/src/docker_modules/bwa/0.7.17/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/BWA/0.7.17 -t 'bwa:0.7.17'
+docker build src/docker_modules/bwa/0.7.17 -t 'bwa:0.7.17'
diff --git a/src/docker_modules/deeptools/3.0.2/docker_init.sh b/src/docker_modules/deeptools/3.0.2/docker_init.sh
index ed0f069b..a2f152d2 100755
--- a/src/docker_modules/deeptools/3.0.2/docker_init.sh
+++ b/src/docker_modules/deeptools/3.0.2/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/deepTools/3.0.2 -t 'deeptools:3.0.2'
+docker build src/docker_modules/deeptools/3.0.2 -t 'deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.1.1/docker_init.sh b/src/docker_modules/deeptools/3.1.1/docker_init.sh
index fb13a0a1..3c6782f0 100755
--- a/src/docker_modules/deeptools/3.1.1/docker_init.sh
+++ b/src/docker_modules/deeptools/3.1.1/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/deepTools/3.1.1 -t 'deeptools:3.1.1'
+docker build src/docker_modules/deeptools/3.1.1 -t 'deeptools:3.1.1'
diff --git a/src/docker_modules/fastqc/0.11.5/docker_init.sh b/src/docker_modules/fastqc/0.11.5/docker_init.sh
index d8d557f5..0c02fb70 100755
--- a/src/docker_modules/fastqc/0.11.5/docker_init.sh
+++ b/src/docker_modules/fastqc/0.11.5/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/FastQC/0.11.5 -t 'fastqc:0.11.5'
+docker build src/docker_modules/fastqc/0.11.5 -t 'fastqc:0.11.5'
diff --git a/src/docker_modules/gatk/4.0.8.1/docker_init.sh b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
index 34c49775..31315f92 100755
--- a/src/docker_modules/gatk/4.0.8.1/docker_init.sh
+++ b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/GATK/4.0.8.1 -t 'gatk:4.0.8.1'
+docker build src/docker_modules/gatk/4.0.8.1 -t 'gatk:4.0.8.1'
diff --git a/src/docker_modules/hisat2/2.0.0/docker_init.sh b/src/docker_modules/hisat2/2.0.0/docker_init.sh
index f497a67a..428e28c4 100755
--- a/src/docker_modules/hisat2/2.0.0/docker_init.sh
+++ b/src/docker_modules/hisat2/2.0.0/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/HISAT2/2.0.0 -t 'hisat2:2.0.0'
+docker build src/docker_modules/hisat2/2.0.0 -t 'hisat2:2.0.0'
diff --git a/src/docker_modules/htseq/0.8.0/docker_init.sh b/src/docker_modules/htseq/0.8.0/docker_init.sh
index 5b8415e2..be46648e 100755
--- a/src/docker_modules/htseq/0.8.0/docker_init.sh
+++ b/src/docker_modules/htseq/0.8.0/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/HTSeq/0.8.0 -t 'htseq:0.8.0'
+docker build src/docker_modules/htseq/0.8.0 -t 'htseq:0.8.0'
diff --git a/src/docker_modules/kallisto/0.43.1/docker_init.sh b/src/docker_modules/kallisto/0.43.1/docker_init.sh
index 8904daee..08241603 100755
--- a/src/docker_modules/kallisto/0.43.1/docker_init.sh
+++ b/src/docker_modules/kallisto/0.43.1/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/Kallisto/0.43.1 -t 'kallisto:0.43.1'
+docker build src/docker_modules/kallisto/0.43.1 -t 'kallisto:0.43.1'
diff --git a/src/docker_modules/kallisto/0.44.0/docker_init.sh b/src/docker_modules/kallisto/0.44.0/docker_init.sh
index a17b82f5..9e9e8c91 100755
--- a/src/docker_modules/kallisto/0.44.0/docker_init.sh
+++ b/src/docker_modules/kallisto/0.44.0/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/Kallisto/0.44.0 -t 'kallisto:0.44.0'
+docker build src/docker_modules/kallisto/0.44.0 -t 'kallisto:0.44.0'
diff --git a/src/docker_modules/macs2/2.1.0/docker_init.sh b/src/docker_modules/macs2/2.1.0/docker_init.sh
index 8af6fd7f..6c56575f 100755
--- a/src/docker_modules/macs2/2.1.0/docker_init.sh
+++ b/src/docker_modules/macs2/2.1.0/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/MACS2/2.1.0 -t 'macs2:2.1.0'
+docker build src/docker_modules/macs2/2.1.0 -t 'macs2:2.1.0'
diff --git a/src/docker_modules/multiqc/1.0/docker_init.sh b/src/docker_modules/multiqc/1.0/docker_init.sh
index 7fb1b64e..4c6de82a 100755
--- a/src/docker_modules/multiqc/1.0/docker_init.sh
+++ b/src/docker_modules/multiqc/1.0/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/MultiQC/1.0 -t 'multiqc:1.0'
+docker build src/docker_modules/multiqc/1.0 -t 'multiqc:1.0'
diff --git a/src/docker_modules/music/6613c53/docker_init.sh b/src/docker_modules/music/6613c53/docker_init.sh
index c6163d6b..5daa39f1 100755
--- a/src/docker_modules/music/6613c53/docker_init.sh
+++ b/src/docker_modules/music/6613c53/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/MUSIC/6613c53 -t 'music:6613c53'
+docker build src/docker_modules/music/6613c53 -t 'music:6613c53'
diff --git a/src/docker_modules/rsem/1.3.0/docker_init.sh b/src/docker_modules/rsem/1.3.0/docker_init.sh
index 5d788282..02d4bf9c 100755
--- a/src/docker_modules/rsem/1.3.0/docker_init.sh
+++ b/src/docker_modules/rsem/1.3.0/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/RSEM/1.3.0 -t 'rsem:1.3.0'
+docker build src/docker_modules/rsem/1.3.0 -t 'rsem:1.3.0'
diff --git a/src/docker_modules/salmon/0.8.2/docker_init.sh b/src/docker_modules/salmon/0.8.2/docker_init.sh
index ea75cf11..5abdc6b0 100755
--- a/src/docker_modules/salmon/0.8.2/docker_init.sh
+++ b/src/docker_modules/salmon/0.8.2/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/Salmon/0.8.2 -t 'salmon:0.8.2'
+docker build src/docker_modules/salmon/0.8.2 -t 'salmon:0.8.2'
diff --git a/src/docker_modules/samtools/1.7/docker_init.sh b/src/docker_modules/samtools/1.7/docker_init.sh
index 31916f45..03dc62e9 100755
--- a/src/docker_modules/samtools/1.7/docker_init.sh
+++ b/src/docker_modules/samtools/1.7/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/SAMtools/1.7 -t 'samtools:1.7'
+docker build src/docker_modules/samtools/1.7 -t 'samtools:1.7'
diff --git a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
index 501f769e..234100e8 100755
--- a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
+++ b/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/SRAtoolkit/2.8.2 -t 'sratoolkit:2.8.2'
+docker build src/docker_modules/sratoolkit/2.8.2 -t 'sratoolkit:2.8.2'
diff --git a/src/docker_modules/tophat/2.1.1/docker_init.sh b/src/docker_modules/tophat/2.1.1/docker_init.sh
index 55e782f2..4dd0937a 100755
--- a/src/docker_modules/tophat/2.1.1/docker_init.sh
+++ b/src/docker_modules/tophat/2.1.1/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/TopHat/2.1.1 -t 'tophat:2.1.1'
+docker build src/docker_modules/tophat/2.1.1 -t 'tophat:2.1.1'
diff --git a/src/docker_modules/trimmomatic/0.36/docker_init.sh b/src/docker_modules/trimmomatic/0.36/docker_init.sh
index dd5c050d..63bcdabf 100755
--- a/src/docker_modules/trimmomatic/0.36/docker_init.sh
+++ b/src/docker_modules/trimmomatic/0.36/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/Trimmomatic/0.36 -t 'trimmomatic:0.36'
+docker build src/docker_modules/trimmomatic/0.36 -t 'trimmomatic:0.36'
diff --git a/src/docker_modules/urqt/d62c1f8/docker_init.sh b/src/docker_modules/urqt/d62c1f8/docker_init.sh
index 225589e0..4c6c5269 100755
--- a/src/docker_modules/urqt/d62c1f8/docker_init.sh
+++ b/src/docker_modules/urqt/d62c1f8/docker_init.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-docker build src/docker_modules/UrQt/d62c1f8 -t 'urqt:d62c1f8'
+docker build src/docker_modules/urqt/d62c1f8 -t 'urqt:d62c1f8'
diff --git a/src/nf_modules/bedtools/tests.sh b/src/nf_modules/bedtools/tests.sh
index d493cdea..61b3cc9c 100755
--- a/src/nf_modules/bedtools/tests.sh
+++ b/src/nf_modules/bedtools/tests.sh
@@ -1,13 +1,13 @@
-./nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
- -c src/nf_modules/BEDtools/fasta_from_bed.config \
+./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 "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
- -c src/nf_modules/BEDtools/fasta_from_bed.config \
+./nextflow src/nf_modules/bedtools/fasta_from_bed.nf \
+ -c src/nf_modules/bedtools/fasta_from_bed.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--bed "data/tiny_dataset/annot/tiny.bed" \
diff --git a/src/nf_modules/bowtie/tests.sh b/src/nf_modules/bowtie/tests.sh
index 3df87dfe..65dfe80e 100755
--- a/src/nf_modules/bowtie/tests.sh
+++ b/src/nf_modules/bowtie/tests.sh
@@ -1,34 +1,34 @@
-./nextflow src/nf_modules/Bowtie/indexing.nf \
- -c src/nf_modules/Bowtie/indexing.config \
+./nextflow src/nf_modules/bowtie/indexing.nf \
+ -c src/nf_modules/bowtie/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-./nextflow src/nf_modules/Bowtie/mapping_single.nf \
- -c src/nf_modules/Bowtie/mapping_single.config \
+./nextflow src/nf_modules/bowtie/mapping_single.nf \
+ -c src/nf_modules/bowtie/mapping_single.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
- -c src/nf_modules/Bowtie/mapping_paired.config \
+./nextflow src/nf_modules/bowtie/mapping_paired.nf \
+ -c src/nf_modules/bowtie/mapping_paired.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/Bowtie/indexing.nf \
- -c src/nf_modules/Bowtie/indexing.config \
+./nextflow src/nf_modules/bowtie/indexing.nf \
+ -c src/nf_modules/bowtie/indexing.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-./nextflow src/nf_modules/Bowtie/mapping_single.nf \
- -c src/nf_modules/Bowtie/mapping_single.config \
+./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"
-./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
- -c src/nf_modules/Bowtie/mapping_paired.config \
+./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"
diff --git a/src/nf_modules/bowtie2/tests.sh b/src/nf_modules/bowtie2/tests.sh
index 01e349a7..bfec0d53 100755
--- a/src/nf_modules/bowtie2/tests.sh
+++ b/src/nf_modules/bowtie2/tests.sh
@@ -1,39 +1,39 @@
-./nextflow src/nf_modules/Bowtie2/indexing.nf \
- -c src/nf_modules/Bowtie2/indexing.config \
+./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 \
+./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 \
+./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 \
+./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 \
+./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 \
+./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" \
diff --git a/src/nf_modules/bwa/tests.sh b/src/nf_modules/bwa/tests.sh
index 8f3c52da..2125e6c3 100755
--- a/src/nf_modules/bwa/tests.sh
+++ b/src/nf_modules/bwa/tests.sh
@@ -1,17 +1,17 @@
-./nextflow src/nf_modules/BWA/indexing.nf \
- -c src/nf_modules/BWA/indexing.config \
+./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 \
+# ./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 \
+./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" \
@@ -19,21 +19,21 @@
if [ -x "$(command -v singularity)" ]; then
-./nextflow src/nf_modules/BWA/indexing.nf \
- -c src/nf_modules/BWA/indexing.config \
+./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 \
+# ./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 \
+./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" \
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
index f6950b96..9100afcc 100755
--- a/src/nf_modules/deeptools/tests.sh
+++ b/src/nf_modules/deeptools/tests.sh
@@ -2,8 +2,8 @@
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"
+./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"
-./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"
+./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"
-./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"
+./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"
diff --git a/src/nf_modules/fastqc/tests.sh b/src/nf_modules/fastqc/tests.sh
index de58b102..1882ded7 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 \
- -c src/nf_modules/FastQC/fastqc_paired.config \
+./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 \
- -c src/nf_modules/FastQC/fastqc_single.config \
+./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 4a2b5ceb..63e4ad51 100755
--- a/src/nf_modules/htseq/tests.sh
+++ b/src/nf_modules/htseq/tests.sh
@@ -1,5 +1,5 @@
-./nextflow src/nf_modules/HTSeq/htseq.nf \
- -c src/nf_modules/HTSeq/htseq.config \
+./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"
diff --git a/src/nf_modules/kallisto/tests.sh b/src/nf_modules/kallisto/tests.sh
index 0f69fcc4..cd87cf00 100755
--- a/src/nf_modules/kallisto/tests.sh
+++ b/src/nf_modules/kallisto/tests.sh
@@ -1,16 +1,16 @@
-./nextflow src/nf_modules/Kallisto/indexing.nf \
- -c src/nf_modules/Kallisto/indexing.config \
+./nextflow src/nf_modules/kallisto/indexing.nf \
+ -c src/nf_modules/kallisto/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-./nextflow src/nf_modules/Kallisto/mapping_single.nf \
- -c src/nf_modules/Kallisto/mapping_single.config \
+./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"
-./nextflow src/nf_modules/Kallisto/mapping_paired.nf \
- -c src/nf_modules/Kallisto/mapping_paired.config \
+./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"
diff --git a/src/nf_modules/multiqc/tests.sh b/src/nf_modules/multiqc/tests.sh
index 0e38a8e9..baa1afaa 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 \
- -c src/nf_modules/MultiQC/multiqc_paired.config \
+./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 \
- -c src/nf_modules/MultiQC/multiqc_single.config \
+./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/music/tests.sh b/src/nf_modules/music/tests.sh
index 7c6ad078..23a62b4f 100755
--- a/src/nf_modules/music/tests.sh
+++ b/src/nf_modules/music/tests.sh
@@ -1,6 +1,6 @@
cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
-./nextflow src/nf_modules/MUSIC/peak_calling_single.nf \
- -c src/nf_modules/MUSIC/peak_calling_single.config \
+./nextflow src/nf_modules/music/peak_calling_single.nf \
+ -c src/nf_modules/music/peak_calling_single.config \
-profile docker \
--fasta "results/training/fasta/*.fasta" \
--bam "results/training/bams/s*.bam" \
diff --git a/src/nf_modules/rsem/tests.sh b/src/nf_modules/rsem/tests.sh
index 7d56b790..bfdba62a 100755
--- a/src/nf_modules/rsem/tests.sh
+++ b/src/nf_modules/rsem/tests.sh
@@ -1,17 +1,17 @@
-./nextflow src/nf_modules/RSEM/indexing.nf \
- -c src/nf_modules/RSEM/indexing.config \
+./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 \
- -c src/nf_modules/RSEM/quantification_single.config \
+./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 \
- -c src/nf_modules/RSEM/quantification_paired.config \
+./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"
diff --git a/src/nf_modules/samtools/tests.sh b/src/nf_modules/samtools/tests.sh
index 9b7ac5e4..96a55e51 100755
--- a/src/nf_modules/samtools/tests.sh
+++ b/src/nf_modules/samtools/tests.sh
@@ -1,20 +1,20 @@
-./nextflow src/nf_modules/SAMtools/sort_bams.nf \
- -c src/nf_modules/SAMtools/sort_bams.config \
+./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 \
- -c src/nf_modules/SAMtools/index_bams.config \
+./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 \
- -c src/nf_modules/SAMtools/split_bams.config \
+./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 \
- -c src/nf_modules/SAMtools/filter_bams.config \
+./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"
diff --git a/src/nf_modules/sratoolkit/tests.sh b/src/nf_modules/sratoolkit/tests.sh
index d8575eb4..0321590e 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 \
- -c src/nf_modules/SRAtoolkit/fastqdump.config \
+./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"
+ --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 cc8e32f4..9992c674 100755
--- a/src/nf_modules/urqt/tests.sh
+++ b/src/nf_modules/urqt/tests.sh
@@ -1,24 +1,24 @@
-./nextflow src/nf_modules/UrQt/trimming_paired.nf \
- -c src/nf_modules/UrQt/trimming_paired.config \
+./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 \
+./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 \
+./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 \
+./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
diff --git a/src/singularity_modules/UrQt/d62c1f8/build.sh b/src/singularity_modules/UrQt/d62c1f8/build.sh
deleted file mode 100755
index e003afad..00000000
--- a/src/singularity_modules/UrQt/d62c1f8/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/UrQt:d62c1f8.sif src/singularity_modules/UrQt/d62c1f8/UrQt.def
-singularity sign bin/UrQt:d62c1f8.sif
diff --git a/src/singularity_modules/bedtools/2.25.0/build.sh b/src/singularity_modules/bedtools/2.25.0/build.sh
index f72bd656..91a1cfe3 100755
--- a/src/singularity_modules/bedtools/2.25.0/build.sh
+++ b/src/singularity_modules/bedtools/2.25.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bedtools:2.25.0.sif src/singularity_modules/BEDtools/2.25.0/BEDtools.def
+sudo singularity build --force bin/bedtools:2.25.0.sif src/singularity_modules/bedtools/2.25.0/bedtools.def
singularity sign bin/bedtools:2.25.0.sif
diff --git a/src/singularity_modules/bowtie/1.2.2/build.sh b/src/singularity_modules/bowtie/1.2.2/build.sh
index 2c7a0e6c..29590dd3 100755
--- a/src/singularity_modules/bowtie/1.2.2/build.sh
+++ b/src/singularity_modules/bowtie/1.2.2/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bowtie:1.2.2.sif src/singularity_modules/Bowtie/1.2.2/Bowtie.def
+sudo singularity build --force bin/bowtie:1.2.2.sif src/singularity_modules/bowtie/1.2.2/bowtie.def
singularity sign bin/bowtie:1.2.2.sif
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/build.sh b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
index 398fb1c7..8d7c7f26 100755
--- a/src/singularity_modules/bowtie2/2.3.4.1/build.sh
+++ b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bowtie2:2.3.4.1.sif src/singularity_modules/Bowtie2/2.3.4.1/Bowtie2.def
+sudo singularity build --force bin/bowtie2:2.3.4.1.sif src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
singularity sign bin/bowtie2:2.3.4.1.sif
diff --git a/src/singularity_modules/bwa/0.7.17/build.sh b/src/singularity_modules/bwa/0.7.17/build.sh
index 26b75eff..91217c0d 100755
--- a/src/singularity_modules/bwa/0.7.17/build.sh
+++ b/src/singularity_modules/bwa/0.7.17/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bwa:0.7.17.sif src/singularity_modules/BWA/0.7.17/BWA.def
+sudo singularity build --force bin/bwa:0.7.17.sif src/singularity_modules/bwa/0.7.17/bwa.def
singularity sign bin/bwa:0.7.17.sif
diff --git a/src/singularity_modules/UrQt/d62c1f8/UrQt.def b/src/singularity_modules/urqt/d62c1f8/UrQt.def
similarity index 100%
rename from src/singularity_modules/UrQt/d62c1f8/UrQt.def
rename to src/singularity_modules/urqt/d62c1f8/UrQt.def
diff --git a/src/singularity_modules/urqt/d62c1f8/build.sh b/src/singularity_modules/urqt/d62c1f8/build.sh
new file mode 100755
index 00000000..81351fcc
--- /dev/null
+++ b/src/singularity_modules/urqt/d62c1f8/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/urqt:d62c1f8.sif src/singularity_modules/urqt/d62c1f8/urqt.def
+singularity sign bin/urqt:d62c1f8.sif
--
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