Merge branch 'update_docker_images' into 'master'

Use minified container images

Closes #105

See merge request zavolan_group/pipelines/rhea!55

README.md

@@ -5,13 +5,16 @@ developed by the [Zavolan lab][zavolan-lab].
 
 Reads are processed, aligned, quantified and analyzed with state-of-the-art
 tools to give meaningful initial insights into various aspects of an RNA-Seq
-library while cutting down on hands-on time for bioinformaticians. For a more detailed description of the individual rules please refer to the [pipeline documentation][pipeline-documentation].    
+library while cutting down on hands-on time for bioinformaticians.
 
-Below is a visual representation of the individual workflow steps ("pe"
+Below is a schematic representation of the individual workflow steps ("pe"
 refers to "paired-end"):
 
 > ![rule_graph][rule-graph]
 
+For a more detailed description of each step, please refer to the [pipeline
+documentation][pipeline-documentation].
+
 ## Requirements
 
 Currently the workflow is only available for Linux distributions. It was tested
@@ -329,4 +332,4 @@ Contaminant sequences | contaminant_seqs
 [singularity-install]: <https://sylabs.io/guides/3.5/admin-guide/installation.html>
 [slurm]: <https://slurm.schedmd.com/documentation.html>
 [zavolan-lab]: <https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/>
-[pipeline-documentation]: pipeline_documentation.md
\ No newline at end of file
+[pipeline-documentation]: pipeline_documentation.md

Snakefile

@@ -147,7 +147,7 @@ rule extract_transcriptome:
             config['log_dir'],
             "{organism}_extract_transcriptome.log")
     singularity:
-        "docker://zavolab/gffread:0.11.7"
+        "docker://zavolab/gffread:0.11.7-slim"
     shell:
         "(gffread \
         -w {output.transcriptome} \
@@ -743,7 +743,7 @@ rule generate_alfa_index:
     threads: 4
 
     singularity: 
-        "docker://zavolab/alfa:1.1.1"
+        "docker://zavolab/alfa:1.1.1-slim"
 
     log: 
         os.path.join(config["log_dir"], "{organism}_{index_size}_generate_alfa_index.log")
@@ -813,7 +813,7 @@ rule alfa_qc:
         name = "{sample}"
 
     singularity:
-        "docker://zavolab/alfa:1.1.1"
+        "docker://zavolab/alfa:1.1.1-slim"
 
     log: 
         os.path.abspath(os.path.join(
@@ -864,7 +864,7 @@ rule alfa_qc_all_samples:
             "alfa_qc_all_samples.{unique}.log"))
 
     singularity:
-        "docker://zavolab/alfa:1.1.1"
+        "docker://zavolab/alfa:1.1.1-slim"
 
     shell:
         """
@@ -897,7 +897,7 @@ rule alfa_concat_results:
             "alfa_qc_all_samples.concat.log"))
 
     singularity:
-        "docker://zavolab/imagemagick:7.0.8"
+        "docker://zavolab/imagemagick:6.9.10-slim"
 
     shell:
         """