diff --git a/README.md b/README.md
index 75f550fdfc6c43c7a49ee5307fd59b0441e97ef5..128870c63743bca5d9315b6219eefc4bb1cfa1d9 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,13 @@
# mir-prepare-annotation
-[Snakemake] workflow to download and prepare the necessary files for smallRNA-seq related pipelines, currently [mir-map](https://git.scicore.unibas.ch/zavolan_group/pipelines/mir-map) and [mir-quant](https://git.scicore.unibas.ch/zavolan_group/pipelines/mir-quant).
+[Snakemake] workflow to download and prepare the necessary files for
+smallRNA-seq related pipelines
+[mir-map](https://git.scicore.unibas.ch/zavolan_group/pipelines/mir-map)
+and
+[mir-quant](https://git.scicore.unibas.ch/zavolan_group/pipelines/mir-quant).
The scheme below is a visual representation of an example run of the
-workflow:
+workflow:
> 
@@ -18,10 +22,19 @@ move into it with:
git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/mir-prepare-annotation.git
cd mir-prepare-annotation
```
+
### Setting up a virtual environment
Workflow dependencies can be conveniently installed with the [Conda][conda]
-package manager. We recommend that you install [Miniconda][miniconda-installation] for your system.
+package manager. We recommend that you install
+[Miniconda][miniconda-installation] for your system.
+
+For improved reproducibility and reusability of the workflow, as well as an
+easy means to run it on a high performance computing (HPC) cluster managed,
+e.g., by [Slurm][slurm], almost all steps of the workflow run in their own
+container. As a consequence, running this workflow has very few individual
+dependencies. It does, however, require that the container engine
+[Singularity][singularity] is installed.
Create and activate the environment with necessary dependencies with conda:
@@ -30,69 +43,83 @@ conda env create -f environment.yml
conda activate mir_pipelines
```
-For improved reproducibility and reusability of the workflow, as well as an
-easy means to run it on a high performance computing (HPC) cluster managed,
-e.g., by [Slurm][slurm], each individual step of the workflow runs in its own container.
-Specifically, containers are created out of [Singularity][singularity] images
-built for each software used within the workflow. As a consequence, running
-this workflow has very few individual dependencies. It does, however, require
-that [Singularity][singularity] to be installed.
+> **NOTE:** If `singularity` is already installed on your system, which is,
+> e.g., frequently the case in HPC environments, make sure to comment out or
+> delete the corresponding line from `environment.yml` prior to the creation
+> of the Conda environment. This will avoid conflicts.
+
+### Testing your installation
+
+Several tests are prepared to check the integrity of the workflow.
-> **NOTE:** `Singularity` is automatically loaded on the sciCORE system. To avoid conflicts, comment out or delete `singularity` in the file `environment.yml` before you create the virtual environment.
+Change into the test directory:
-## Testing
-Several tests are prepared to check the integrity of the workflow.
-Move into `test/` directory:
```bash
cd test/
```
-## DAG and rule graph
-Execute the following commands to generete DAG and rule graph images. Outputs will be found in `images/` folder.
+#### DAG and rule graph
+
+Execute the following commands to generete DAG and rule graph images. Outputs
+will be found in `images/` folder.
+
```bash
./test_dag.sh
./test_rule_graph.sh
```
-### Run workflow on local machine
+
+#### Run workflow on local machine
+
Execute the following command to run the test workflow on your local machine:
+
```bash
./test_workflow_local.sh
```
-### Run workflow via Slurm
-Execute the following command to run the test workflow on a Slurm-managed high-performance computing (HPC) cluster::
+#### Run workflow via Slurm
+
+Execute the following command to run the test workflow on a Slurm-managed
+high-performance computing (HPC) cluster:
+
```bash
./test_workflow_slurm.sh
```
## Usage
-Assuming that you are currently inside the repository's root directory...
+Assuming that you are currently inside the repository's root directory, change
+to the execution directory:
-* To run the pipeline with your own samples:
```bash
cd RUN_JOB
```
-Before running the pipeline adjust the parameters in `config.yaml`file.
+
+Before running the pipeline adjust the parameters in file `config.yaml`. We
+recommend that you create a copy of it for each run.
+
To start pipeline execution locally:
+
```bash
./run_workflow_local.sh
```
-To start pipeline execution in Slurm:
-> *Recommended due to resources needs*
+
+To start pipeline execution via Slurm:
```bash
./run_workflow_slurm.sh
```
-After succesfully execution of the workflow results and logs outputs will be found in `results/` and `logs/` directories.
-
-> **NOTE:** Depending on the configuration of your Slurm installation or if using a different workflow manager,
-> you may need to adapt file `cluster.json` (located in root directory) and the arguments to options `--config` and `--cores` in file
-> `run_workflow_slurm.sh`, located in RUN_JOB directory. Consult the manual of your workload manager as well as the section of the
-> Snakemake manual dealing with [cluster execution].
+> *This is strongly recommended due to excessive resource needs of some tools!*
+After succesful execution of the workflow, results and logs will be found in
+`results/` and `logs/` directories, respectively.
+> **NOTE:** Depending on the configuration of your Slurm installation or if
+> using a different batch scheduling system, you may need to adapt file
+> `cluster.json` (located in root directory) and the arguments to options
+> `--config` and `--cores` in file `run_workflow_slurm.sh`, located in the
+> `RUN_JOB` directory. Consult the manual of your batch scheduling system, as
+> well as the section of the Snakemake manual dealing with [cluster execution].
[conda]: <https://docs.conda.io/projects/conda/en/latest/index.html>
[cluster execution]: <https://snakemake.readthedocs.io/en/stable/executing/cluster-cloud.html#cluster-execution>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 439febdd589cb478a60be390912046a177f0e66e..8ea8ac09bc8a336c75c4c5b20b50032c6d371bd7 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,123 +1,145 @@
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="326.5,-190.104 323,-180.104 319.5,-190.104 326.5,-190.104"/>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="348.252,-257.051 338.883,-252.104 343.122,-261.814 348.252,-257.051"/>
+<g id="edge11" class="edge">
+<title>9->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M412.079,-287.8314C403.3471,-279.219 392.7683,-268.7851 383.2577,-259.4048"/>
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diff --git a/images/workflow_dag.svg b/images/workflow_dag.svg
index 8383d3e22d755194681385e4532ee949f29730dd..5dce513383ddfd4c32f0384dc1b09203cb0b1e3b 100644
--- a/images/workflow_dag.svg
+++ b/images/workflow_dag.svg
@@ -1,127 +1,149 @@
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+ viewBox="0.00 0.00 555.50 337.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
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<title>snakemake_dag</title>
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-<text text-anchor="middle" x="323" y="-87.5" font-family="sans" font-size="10.00">generate_segemehl_index_transcriptome</text>
+<g id="node2" class="node">
+<title>1</title>
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+<text text-anchor="middle" x="357.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">generate_segemehl_index_transcriptome</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="284.685,-41.1959 275.394,-36.1043 279.482,-45.8787 284.685,-41.1959"/>
+<g id="edge1" class="edge">
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-<text text-anchor="middle" x="85" y="-87.5" font-family="sans" font-size="10.00">generate_segemehl_index_genome</text>
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+<path fill="none" stroke="#59d856" stroke-width="2" d="M179,-108C179,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 179,-72 179,-72 185,-72 191,-78 191,-84 191,-84 191,-96 191,-96 191,-102 185,-108 179,-108"/>
+<text text-anchor="middle" x="95.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">generate_segemehl_index_genome</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="224.896,-36.8112 232.881,-29.8475 222.297,-30.3118 224.896,-36.8112"/>
+<g id="edge2" class="edge">
+<title>2->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M144.202,-71.8314C177.6557,-59.3512 221.3625,-43.0461 251.8709,-31.6648"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="253.1368,-34.9282 261.2827,-28.1536 250.69,-28.3697 253.1368,-34.9282"/>
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+<g id="node4" class="node">
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+<text text-anchor="middle" x="514.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">gtftobed</text>
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-<text text-anchor="middle" x="198" y="-159.5" font-family="sans" font-size="10.00">create_header_genome</text>
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+<text text-anchor="middle" x="219.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">create_header_genome</text>
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-<text text-anchor="middle" x="323" y="-159.5" font-family="sans" font-size="10.00">trim_fasta</text>
+<g id="node6" class="node">
+<title>5</title>
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+<text text-anchor="middle" x="357.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">trim_fasta</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="326.5,-118.104 323,-108.104 319.5,-118.104 326.5,-118.104"/>
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+<text text-anchor="middle" x="219.5" y="-317" font-family="sans" font-size="10.00" fill="#000000">genome_process</text>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M207.097,-287.6883C192.065,-262.3653 166.0689,-218.2504 144.5,-180 132.7032,-159.0794 119.7218,-135.1953 110.0859,-117.291"/>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="201.5,-190.295 198,-180.296 194.5,-190.296 201.5,-190.295"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M219.5,-287.8208C219.5,-262.3635 219.5,-219.0008 219.5,-190.4249"/>
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-<text text-anchor="middle" x="453" y="-231.5" font-family="sans" font-size="10.00">get_exons_gtf</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M535.5,-252C535.5,-252 473.5,-252 473.5,-252 467.5,-252 461.5,-246 461.5,-240 461.5,-240 461.5,-228 461.5,-228 461.5,-222 467.5,-216 473.5,-216 473.5,-216 535.5,-216 535.5,-216 541.5,-216 547.5,-222 547.5,-228 547.5,-228 547.5,-240 547.5,-240 547.5,-246 541.5,-252 535.5,-252"/>
+<text text-anchor="middle" x="504.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">get_exons_gtf</text>
</g>
<!-- 7->3 -->
-<g id="edge7" class="edge"><title>7->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M454.447,-215.871C456.493,-191.67 460.25,-147.211 462.685,-118.393"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="466.193,-118.449 463.547,-108.189 459.218,-117.859 466.193,-118.449"/>
+<g id="edge7" class="edge">
+<title>7->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M505.7665,-215.7623C507.4721,-191.201 510.5245,-147.2474 512.531,-118.3541"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="516.0425,-118.3081 513.2438,-108.0896 509.0593,-117.8231 516.0425,-118.3081"/>
</g>
<!-- 8->5 -->
-<g id="edge9" class="edge"><title>8->5</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="326.5,-190.104 323,-180.104 319.5,-190.104 326.5,-190.104"/>
+<g id="edge9" class="edge">
+<title>8->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M357.5,-215.8314C357.5,-208.131 357.5,-198.9743 357.5,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="361.0001,-190.4132 357.5,-180.4133 354.0001,-190.4133 361.0001,-190.4132"/>
</g>
<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" stroke-dasharray="5,2" d="M475.5,-329C475.5,-329 346.5,-329 346.5,-329 340.5,-329 334.5,-323 334.5,-317 334.5,-317 334.5,-300 334.5,-300 334.5,-294 340.5,-288 346.5,-288 346.5,-288 475.5,-288 475.5,-288 481.5,-288 487.5,-294 487.5,-300 487.5,-300 487.5,-317 487.5,-317 487.5,-323 481.5,-329 475.5,-329"/>
-<text text-anchor="middle" x="411" y="-317" font-family="sans" font-size="10.00">filter_anno_gtf</text>
-<text text-anchor="middle" x="411" y="-306" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
-<text text-anchor="middle" x="411" y="-295" font-family="sans" font-size="10.00">prefix_name: GRCh38.98_chrY</text>
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M517,-329C517,-329 378,-329 378,-329 372,-329 366,-323 366,-317 366,-317 366,-300 366,-300 366,-294 372,-288 378,-288 378,-288 517,-288 517,-288 523,-288 529,-294 529,-300 529,-300 529,-317 529,-317 529,-323 523,-329 517,-329"/>
+<text text-anchor="middle" x="447.5" y="-317" font-family="sans" font-size="10.00" fill="#000000">filter_anno_gtf</text>
+<text text-anchor="middle" x="447.5" y="-306" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<text text-anchor="middle" x="447.5" y="-295" font-family="sans" font-size="10.00" fill="#000000">prefix_name: GRCh38.98_chrY</text>
</g>
<!-- 9->7 -->
-<g id="edge10" class="edge"><title>9->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M422.477,-287.689C427.236,-279.474 432.822,-269.83 437.906,-261.055"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="440.982,-262.727 442.967,-252.319 434.925,-259.218 440.982,-262.727"/>
+<g id="edge10" class="edge">
+<title>9->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M463.3777,-287.7476C469.935,-279.177 477.6095,-269.1463 484.5413,-260.0864"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="487.3483,-262.1775 490.645,-252.1087 481.7888,-257.924 487.3483,-262.1775"/>
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<!-- 9->8 -->
-<g id="edge12" class="edge"><title>9->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M386.954,-287.689C376.061,-278.715 363.098,-268.036 351.7,-258.645"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="353.673,-255.736 343.729,-252.078 349.222,-261.138 353.673,-255.736"/>
+<g id="edge12" class="edge">
+<title>9->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M422.43,-287.7476C411.548,-278.7398 398.7176,-268.119 387.348,-258.7076"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="389.3113,-255.7891 379.3762,-252.1087 384.8477,-261.1814 389.3113,-255.7891"/>
</g>
</g>
</svg>
diff --git a/test/expected_output.files b/test/expected_output.files
index 6615521a6e1de3f32590e0d861f33127ab1e0ef9..a8d99461bd457faff08d50f595ab4d9fd79791c3 100644
--- a/test/expected_output.files
+++ b/test/expected_output.files
@@ -6,5 +6,4 @@ results/homo_sapiens/GRCh38.98_chrY/gene_annotations.filtered.gtf
results/homo_sapiens/GRCh38.98_chrY/exons.gtf
results/homo_sapiens/GRCh38.98_chrY/transcriptome.fa
results/homo_sapiens/GRCh38.98_chrY/exons.bed
-results/homo_sapiens/GRCh38.98_chrY/headerOfCollapsedFasta.sam
-results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
\ No newline at end of file
+results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
diff --git a/test/expected_output.md5 b/test/expected_output.md5
index ddc2e4d3f15c271c71372d76461619d96c999710..57dc755124001949c4accb0e5dd2c72c77366db2 100644
--- a/test/expected_output.md5
+++ b/test/expected_output.md5
@@ -6,5 +6,4 @@ f37a213f94d11bf2260f50f2c9f199d2 results/homo_sapiens/GRCh38.98_chrY/genome.pro
6fe52e2e126ef2e0c368fb1bf267f453 results/homo_sapiens/GRCh38.98_chrY/exons.gtf
5ab1c2f39ab35fabc6673c73beb3097b results/homo_sapiens/GRCh38.98_chrY/transcriptome.fa
51ac61c61825929f8f05c4b4f821f04d results/homo_sapiens/GRCh38.98_chrY/exons.bed
-7027e0b45c8e46ef79f1cb234fa3b839 results/homo_sapiens/GRCh38.98_chrY/headerOfCollapsedFasta.sam
-11b0b7c50160aa8837dd92eda516c124 results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
\ No newline at end of file
+11b0b7c50160aa8837dd92eda516c124 results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
diff --git a/test/test_workflow_local.sh b/test/test_workflow_local.sh
index 69b9942212603288c3eb8140d35b3b1001da38b2..37b051b866b4d59bf58d675f5c14f0bcc298304d 100755
--- a/test/test_workflow_local.sh
+++ b/test/test_workflow_local.sh
@@ -3,8 +3,8 @@
# Tear down test environment
cleanup () {
rc=$?
- #rm -rf .snakemake/
- #rm -rf logs/
+ rm -rf .snakemake/
+ rm -rf logs/
rm -rf results/
cd $user_dir
echo "Exit status: $rc"