Merge pull request #11 from cokelaer/dev

Use new rulegraph wrapper and graphviz apptainer
sequana · May 17, 2023 · 97e2566 · 97e2566
2 parents 42ca6d5 + 3ae26ba
commit 97e2566
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Showing 6 changed files with 51 additions and 17 deletions.
diff --git a/README.rst b/README.rst
@@ -132,6 +132,8 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.7.0     * Use new rulegraph wrapper and new graphviz apptainer
+1.6.2     * slight refactorisation to use rulegraph wrapper
 1.6.1     * pin sequana version to 1.4.4 to force usage of new fastqc module
             to fix falco. Updated config documentation.
 1.6.0     * Fixed falco output error and use singularity containers

diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1,2 @@
 sequana>=0.14.4
-sequana_pipetools>=0.9.1
+sequana_pipetools>=0.12.2
diff --git a/sequana_pipelines/fastqc/config.yaml b/sequana_pipelines/fastqc/config.yaml
@@ -18,12 +18,18 @@ input_pattern: '*fastq.gz'
 # in special cases, sample names can be extracted with a pattern
 #sample_pattern: '{sample}.fastq.gz'
 
+
+apptainers:
+    falco: "https://zenodo.org/record/7014954/files/falco_1.0.0.img"
+    fastqc: "https://zenodo.org/record/7923780/files/fastqc_0.12.1.img"
+    graphviz: "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
+
+
 ##############################################################################
 # general section
 #
 # Choose one of the standard method to perform QC of your fastq data
 #
-# method_choice__ = ['fastqc', 'falco']
 general:
     method_choice: fastqc
 

diff --git a/sequana_pipelines/fastqc/fastqc.rules b/sequana_pipelines/fastqc/fastqc.rules
@@ -27,6 +27,8 @@ configfile: "config.yaml"
 
 manager = PipelineManager("fastqc", config)
 
+sequana_wrapper_branch = "main"
+
 # This is just for information. Not used in the pipeline but only for HTML rpeort
 # do we have illumina paired data with tag _R1_ ?
 R1 = [1 for x in manager.samples.values() if "_R1_" in x.split("/")[-1]]
@@ -67,8 +69,10 @@ if 'general' in config and 'method_choice' in config['general'] and \
     METHOD = "falco"
 
     rule falco:
-        input: manager.getrawdata()
-        output: "samples/{sample}/summary.txt"
+        input:
+            manager.getrawdata()
+        output:
+            "samples/{sample}/summary.txt"
         log:
             "samples/{sample}/falco.log"
         threads:
@@ -77,19 +81,21 @@ if 'general' in config and 'method_choice' in config['general'] and \
             options=config['falco']['options'],
             working_directory="samples/{sample}"
         container:
-            "https://zenodo.org/record/7014954/files/falco_1.0.0.img"
+            config['apptainers']['falco']
         resources:
             **config['falco']['resources']
         wrapper:
-            "main/wrappers/falco"
+            f"{sequana_wrapper_branch}/wrappers/falco"
     __multiqc__input = expand("samples/{sample}/summary.txt", sample=manager.samples)
 
 else:
     METHOD = "fastqc"
 
     rule fastqc:
-        input: manager.getrawdata()
-        output: "samples/{sample}/fastqc.done"
+        input:
+            manager.getrawdata()
+        output:
+            "samples/{sample}/fastqc.done"
         log:
             "samples/{sample}/fastqc.log"
         threads:
@@ -100,9 +106,9 @@ else:
         resources:
             **config['fastqc']['resources']
         container:
-            "https://zenodo.org/record/7015004/files/fastqc_0.11.9-py3.img"
+            config['apptainers']['fastqc']
         wrapper:
-            "main/wrappers/fastqc"
+            f"{sequana_wrapper_branch}/wrappers/fastqc"
     __multiqc__input = expand("samples/{sample}/fastqc.done", sample=manager.samples)
 
 
@@ -170,11 +176,28 @@ if config['multiqc']['do']:
            "main/wrappers/multiqc"
 
 
-# ====================================================================== rulegraph 
-sequana_rulegraph_mapper = {}
-if config['multiqc']['do']:
-    sequana_rulegraph_mapper["multiqc"] = "../multiqc/multiqc_report.html"
-include: sm.modules['rulegraph']
+# ====================================================================== rulegraph
+
+rule rulegraph:
+    input: str(manager.snakefile)
+    output:
+        svg = "rulegraph/rulegraph.dot"
+    params:
+        mapper = {"multiqc": "../multiqc/multiqc_report.html"} if config['multiqc']['do'] else {},
+        configname = "config.yaml"
+    wrapper:
+        f"{sequana_wrapper_branch}/wrappers/rulegraph"
+
+
+rule dot2svg:
+    input:
+        "rulegraph/rulegraph.dot"
+    output:
+        ".sequana/rulegraph.svg"
+    container:
+        config['apptainers']['graphviz']
+    shell:
+        """dot -Tsvg {input} -o {output}"""
 
 
 rule plotting_and_stats:

diff --git a/sequana_pipelines/fastqc/schema.yaml b/sequana_pipelines/fastqc/schema.yaml
@@ -23,6 +23,9 @@ mapping:
             "resources":
                 type: any
                 required: true
+    "apptainers":
+        type: any
+
 
     "multiqc":
         type: map

diff --git a/setup.py b/setup.py
@@ -4,8 +4,8 @@
 import subprocess
 
 _MAJOR               = 1
-_MINOR               = 6
-_MICRO               = 1
+_MINOR               = 7
+_MICRO               = 0
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)