Update

CONTRIBUTING.md

@@ -54,7 +54,7 @@ git clone git@github.com:jfnavarro/st_pipeline.git
 ```
 
 3. Ensure [poetry](https://python-poetry.org/docs/) is installed.
-4. Ensure [STAR](https://github.com/alexdobin/STAR) is installed.
+4. Ensure [STAR](https://github.com/alexdobin/STAR) and [samtools](https://www.htslib.org/) are installed.
 5. Install dependencies and start your virtualenv:
 
 ``` console

Dockerfile

@@ -6,7 +6,7 @@ ENV POETRY_VERSION=1.7.2 \
     POETRY_NO_INTERACTION=1 \
     PATH="/root/.local/bin:$PATH"
 
-# Install system dependencies, Poetry, and STAR
+# Install system dependencies, Poetry, STAR, and Samtools
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
        build-essential \
@@ -18,14 +18,25 @@ RUN apt-get update \
        gcc \
        wget \
        unzip \
+       zlib1g-dev \
+       libbz2-dev \
+       liblzma-dev \
+       libcurl4-gnutls-dev \
     && wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.10b.zip \
     && unzip 2.7.10b.zip \
     && cd STAR-2.7.10b/source \
     && make STAR \
     && mv STAR /usr/local/bin/ \
     && cd /app \
+    && wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 \
+    && tar -xjf samtools-1.17.tar.bz2 \
+    && cd samtools-1.17 \
+    && ./configure \
+    && make \
+    && make install \
+    && cd /app \
     && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* 2.7.10b.zip STAR-2.7.10b
+    && rm -rf /var/lib/apt/lists/* 2.7.10b.zip STAR-2.7.10b samtools-1.17 samtools-1.17.tar.bz2
 
 # Set working directory
 WORKDIR /app

docs/installation.md

@@ -5,11 +5,12 @@ Python 3.10, 3.11 or 3.12 is required.
 ## Requirements
 
 The ST Pipeline requires [STAR][] installed in the system (minimum version 2.5.4 if you use a ST Pipeline version >= 1.6.0).
+The ST Pipeline requires [samtools][] installed in the system.
 
-If you use anaconda you can install STAR with:
+If you use anaconda you can install STAR and samtools with:
 
-```bash
-conda install -c bioconda star
+``` console
+conda install -c bioconda star samtools
 ```
 
 The ST Pipeline needs a computer with at least 32GB of RAM (depending on the size of the genome) and 8 cpu cores.
@@ -131,6 +132,7 @@ st_pipeline_run --help
 ```
 
   [STAR]: https://github.com/alexdobin/STAR
+  [samtools]: https://www.htslib.org/
   [pip]: https://pip.pypa.io
   [Python installation guide]: http://docs.python-guide.org/en/latest/starting/installation/
   [Github repo]: https://github.com/jfnavarro/st_pipeline/

docs/usage.md

@@ -241,7 +241,7 @@ st_pipeline_run [options] fastq_file_fw fastq_file_rv
 
 An example run would be:
 
-```bash
+```console
 st_pipeline_run --expName test --ids ids_file.txt \
   --ref-map path_to_index --htseq-no-ambiguous --log-file log_file.txt --output-folder /home/me/results \
   --ref-annotation annotation_file.gtf --contaminant-index path_to_cont_index file1.fastq file2.fastq
@@ -270,7 +270,7 @@ If you used an Ensembl annotation file and you would like change
 the output file so it contains gene ids/names instead of Ensembl ids.
 You can use the script `convertEnsemblToNames` that comes with the ST Pipeline
 
-```bash
+```console
 convertEnsemblToNames --annotation path_to_annotation_file --output st_data_updated.tsv st_data.tsv
 ```
 
@@ -279,7 +279,7 @@ convertEnsemblToNames --annotation path_to_annotation_file --output st_data_upda
 If you used different indexes to sequence and need to merge the fastq files
 you can use the script `merge_fastq` that comes with the ST Pipeline
 
-```bash
+```console
 merge_fastq --run-path path_to_run_folder --out-path path_to_output --identifiers S1 S2 S3 S4
 ```
 
@@ -291,7 +291,7 @@ If you want to remove from the dataset (matrix in TSV) genes corresponding
 to certain gene types (For instance to keep only protein_coding). You can do
 so with the script `filter_gene_type_matrix` that comes with the ST Pipeline
 
-```bash
+```console
 filter_gene_type_matrix --gene-types-keep protein-coding --annotation path_to_annotation_file stdata.tsv
 ```
 
@@ -305,7 +305,7 @@ If you want to remove spots from a dataset (matrix in TSV) for instance
 to keep only spots inside the tissue. You can do so with the script `adjust_matrix_coordinates`
 that comes with the ST Pipeline
 
-```bash
+```console
 adjust_matrix_coordinates --outfile new_stdata.tsv --coordinates-file coordinates.txt stdata.tsv
 ```
 
@@ -323,13 +323,13 @@ can update the coordinates in the matrix choosing for the new array or pixel coo
 The ST Pipeline generate useful stats/QC information in the LOG file but if you
 want to obtain more detailed information about the quality of the data, you can run the following script:
 
-```bash
+```console
 st_qa stdata.tsv
 ```
 
 If you want to perform quality stats on multiple datasets you can run:
 
-```bash
+```console
 multi_qa stdata1.tsv stadata2.tsv stdata3.tsv stdata4.tsv
 ```