version update

.test/makefile

@@ -12,6 +12,7 @@ snakefiles := \
 	"../workflow/rules/multiqc.smk" \
 	"../workflow/rules/fastp.smk" \
 	"../workflow/rules/picard_metrics.smk" \
+	"../workflow/rules/samtools_stats.smk" \
 	"../workflow/rules/fair_genome_indexer_pipeline.smk" \
 	"../workflow/rules/common.smk" \
 	"../workflow/Snakefile"

CHANGELOG.md

@@ -1,8 +1,15 @@
 # 2.2.5
 
+## Features:
+
+* Update fair_genome_indexer to version 2.3.0
+* Samtools stats added to report
+
 ## Fix:
 
 * Report main page too large
+* Fix error removing Bowtie2 QC from MultiQC report
+* Fix error making fastp reports non reachable in MultiQC
 
 # 2.2.4
 

workflow/Snakefile

@@ -9,6 +9,7 @@ if config.get("load_fair_genome_indexer", True):
 
 include: "rules/bowtie2_sambamba_meta.smk"
 include: "rules/picard_metrics.smk"
+include: "rules/samtools_stats.smk"
 include: "rules/multiqc.smk"
 
 

workflow/rules/common.smk

@@ -251,7 +251,12 @@ def get_multiqc_report_input(
     Return (Dict[str, List[str]]):
     Dictionnary of all input files as required by MultiQC's snakemake-wrapper
     """
-    results: Dict[str, List[str]] = {"picard_qc": [], "fastp": [], "bowtie2": []}
+    results: Dict[str, List[str]] = {
+        "picard_qc": [],
+        "fastp": [],
+        "bowtie2": [],
+        "samtools": [],
+    }
     datatype: str = "dna"
     sample_iterator = zip(
         samples.sample_id,
@@ -275,18 +280,17 @@ def get_multiqc_report_input(
             snakemake.io.Wildcards(fromdict={"sample": sample}), samples
         )
         if sample_data.get("downstream_file"):
-            results["fastp"].append(f"tmp/fastp/report_pe/{sample}.json")
-            results["fastp"].append(f"results/QC/report_pe/{sample}.html")
-            # results["fastp"].append(f"tmp/fastp/trimmed/{sample}.1.fastq")
-            # results["fastp"].append(f"tmp/fastp/trimmed/{sample}.2.fastq")
+            results["fastp"].append(f"tmp/fastp/report_pe/{sample}.fastp.json")
         else:
-            results["fastp"].append(f"tmp/fastp/report_se/{sample}.json")
-            results["fastp"].append(f"results/QC/report_se/{sample}.html")
-            # results["fastp"].append(f"tmp/fastp/trimmed/{sample}.fastq")
+            results["fastp"].append(f"tmp/fastp/report_se/{sample}.fastp.json")
 
-        results[
-            "bowtie2"
-        ] = f"logs/bowtie2/align/{species}.{build}.{release}.{datatype}/{sample}.log"
+        results["bowtie2"].append(
+            f"logs/bowtie2/align/{species}.{build}.{release}.{datatype}/{sample}.log"
+        )
+
+        results["samtools"].append(
+            f"tmp/samtools/{species}.{build}.{release}.{datatype}/{sample}.txt"
+        )
 
     return results
 

workflow/rules/fair_genome_indexer_pipeline.smk

@@ -1,6 +1,6 @@
 module fair_genome_indexer:
     snakefile:
-        github("tdayris/fair_genome_indexer", path="workflow/Snakefile", tag="2.2.0")
+        github("tdayris/fair_genome_indexer", path="workflow/Snakefile", tag="2.3.0")
     config:
         {"genomes": config["genomes"]}
 

workflow/rules/fastp.smk

@@ -14,7 +14,7 @@ rule fastp_trimming_pair_ended:
             caption="../report/fastp.rst",
             category="Quality Controls",
         ),
-        json=temp("tmp/fastp/report_pe/{sample}.json"),
+        json=temp("tmp/fastp/report_pe/{sample}.fastp.json"),
     log:
         "logs/fastp/{sample}.log",
     benchmark:
@@ -34,4 +34,4 @@ use rule fastp_trimming_pair_ended as fastp_trimming_single_ended with:
             caption="../report/fastp.rst",
             category="Quality Controls",
         ),
-        json=temp("tmp/fastp/report_se/{sample}.json"),
+        json=temp("tmp/fastp/report_se/{sample}.fastp.json"),

workflow/rules/samtools_stats.smk

@@ -0,0 +1,14 @@
+rule samtools_stats:
+    input:
+        bam="results/{species}.{build}.{release}.{datatype}/Mapping/{sample}.bam",
+        bai="results/{species}.{build}.{release}.{datatype}/Mapping/{sample}.bam.bai",
+    output:
+        temp("tmp/samtools/{species}.{build}.{release}.{datatype}/{sample}.txt"),
+    log:
+        "logs/samtools/{species}.{build}.{release}.{datatype}/{sample}.log",
+    benchmark:
+        "benchmark/samtools/{species}.{build}.{release}.{datatype}/{sample}.tsv"
+    params:
+        extra="",
+    wrapper:
+        f"{snakemake_wrappers_version}/bio/samtools/stats"