feat: qm report (#95)

* fix: typo * feat: include qualimap report in snakemake report * refactor: removed compress rules * style: changed names to better reflect their purpose * refactor: removed localrule declaration from rules that no longer exist * fix: profile uses new rule names * style: report viewability and renamed rule parameters to match their rules * style: changed l2fc threshold and improved naming * fix: config keys for test diles, formatting * fix: input path * Update workflow/rules/qc.smk no string detour, just taking config from config dir Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * style: samstats -> bamstats in output directory * fix: accomodating for previous change in the all rule --------- Co-authored-by: Christian Meesters <[email protected]> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: cmeesters <[email protected]>
snakemake-workflows · Oct 11, 2024 · 3782c40 · 3782c40
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diff --git a/.test/config-simple/config.yml b/.test/config-simple/config.yml
@@ -39,10 +39,10 @@ maximum_secondary: 100
 secondary_score_ratio: 1.0
 
 # Samtools view opts, "-b" creates BAM from SAM.
-sview_opts: "-b"
+samtobam_opts: "-b"
 
 # Samtools sort opts,
-ssort_opts: ""
+bamsort_opts: ""
 
 # Salmon library type
 salmon_libtype: "U"
@@ -51,7 +51,7 @@ salmon_libtype: "U"
 # QC options
 
 # Samtools stats opts
-sstats_opts: ""
+bamstats_opts: ""
 
 # Count filtering options - customize these according to your experimental design:
 

diff --git a/config/Mainz-MogonNHR/config.yml b/config/Mainz-MogonNHR/config.yml
@@ -37,10 +37,10 @@ maximum_secondary: 100
 secondary_score_ratio: 1.0
 
 # Samtools view opts, "-b" creates BAM from SAM.
-sview_opts: "-b"
+samtobam_opts: "-b"
 
 # Samtools sort opts,
-ssort_opts: ""
+bamsort_opts: ""
 
 # Salmon library type
 salmon_libtype: "U"
@@ -49,7 +49,7 @@ salmon_libtype: "U"
 # QC options
 
 # Samtools stats opts
-sstats_opts: ""
+bamstats_opts: ""
 
 # Count filtering options - customize these according to your experimental design:
 
@@ -71,7 +71,7 @@ design_factors:
   - "condition"
 #
 # The (log2) log fold change under the null hypothesis. (default: 0).
-lfc_null: 0.1
+lfc_null: 1
 #
 # The alternative hypothesis for computing wald p-values. By default,
 # the normal Wald test assesses deviation of the estimated log fold

diff --git a/workflow/profile/Mainz-MogonNHR/config.yaml b/workflow/profile/Mainz-MogonNHR/config.yaml
@@ -39,22 +39,22 @@ set-resources:
         mem_mb_per_cpu: 1800
         runtime: "1h"
 
-    sam_sort:
+    bam_sort:
         cpus_per_task: 4
         mem_mb_per_cpu: 7200
         runtime: "2h"
 
-    sam_view:
+    sam_to_bam:
         cpus_per_task: 1
         mem_mb_per_cpu: 1800
         runtime: "1h"
 
-    sam_index:
+    bam_index:
         cpus_per_task: 8
         mem_mb_per_cpu: 1800
         runtime: "30m"
 
-    sam_stats:
+    bam_stats:
         cpus_per_task: 8
         mem_mb_per_cpu: 1800
         runtime: "30m"

diff --git a/workflow/report/nanoplot_all_samples_report.rst b/workflow/report/nanoplot_all_samples_report.rst
@@ -1 +1 @@
-Full `NanoPlot, <https://github.com/wdecoster/NanoPlot>`_ sequencing quality report for total samples .
+Full `NanoPlot, <https://github.com/wdecoster/NanoPlot>`_ sequencing quality report for total samples.
diff --git a/workflow/report/qualimap.rst b/workflow/report/qualimap.rst
@@ -0,0 +1 @@
+Full `QualiMap, <http://qualimap.conesalab.org/doc_html/analysis.html#bam-qc>`_ BAMQC alignment quality report for total samples.
diff --git a/workflow/rules/alignmod.smk b/workflow/rules/alignmod.smk
@@ -1,24 +1,24 @@
-rule sam_view:
+rule sam_to_bam:
     input:
         sam="alignments/{sample}.sam",
     output:
-        "sorted_alignments/{sample}.bam",
+        "alignments/{sample}.bam",
     log:
-        "logs/samtools/samview_{sample}.log",
+        "logs/samtools/samtobam_{sample}.log",
     params:
-        extra=f'{config["sview_opts"]}',
+        extra=f'{config["samtobam_opts"]}',
     wrapper:
         "v3.13.4/bio/samtools/view"
 
 
-rule sam_sort:
+rule bam_sort:
     input:
-        sam="alignments/{sample}.sam",
+        bam="alignments/{sample}.bam",
     output:
         "sorted_alignments/{sample}_sorted.bam",
     log:
-        "logs/samtools/samsort_{sample}.log",
+        "logs/samtools/bamsort_{sample}.log",
     params:
-        extra=f'{config["ssort_opts"]}',
+        extra=f'{config["bamsort_opts"]}',
     wrapper:
         "v3.13.4/bio/samtools/sort"
diff --git a/workflow/rules/commons.smk b/workflow/rules/commons.smk
@@ -65,10 +65,14 @@ def aggregate_input(samples):
 def rule_all_input():
     all_input = list()
     all_input.append("versions.txt")
-    all_input.extend(expand("QC/NanoPlot/{sample}.tar.gz", sample=samples["sample"]))
-    all_input.append("QC/NanoPlot/all_samples.tar.gz")
-    all_input.extend(expand("QC/samstats/{sample}.txt", sample=samples["sample"]))
-    all_input.extend(expand("QC/qualimap/{sample}.tar.gz", sample=samples["sample"]))
+    all_input.extend(
+        expand("NanoPlot/{sample}/NanoPlot-report.html", sample=samples["sample"])
+    )
+    all_input.append("NanoPlot/all_samples/NanoPlot-report.html")
+    all_input.extend(expand("QC/bamstats/{sample}.txt", sample=samples["sample"]))
+    all_input.extend(
+        expand("qualimap/{sample}/qualimapReport.html", sample=samples["sample"])
+    )
     all_input.extend(
         expand("counts/{sample}_salmon/quant.sf", sample=samples["sample"])
     )

diff --git a/workflow/rules/diffexp.smk b/workflow/rules/diffexp.smk
@@ -6,33 +6,51 @@ rule de_analysis:
             "de_analysis/dispersion_graph.svg",
             category="Results",
             caption="../report/dispersion_graph.rst",
+            labels={
+                "figure": "Dispersion graph",
+            },
         ),
         ma_graph=report(
             "de_analysis/ma_graph.svg",
             category="Results",
             caption="../report/ma_graph.rst",
+            labels={
+                "figure": "MA plot",
+            },
         ),
         de_heatmap=report(
             "de_analysis/heatmap.svg",
             category="Results",
             caption="../report/heatmap.rst",
+            labels={
+                "figure": "Gene heatmap",
+            },
         ),
         correlation_matrix=report(
             "de_analysis/correlation_matrix.svg",
             category="Results",
             caption="../report/correlation_matrix.rst",
+            labels={
+                "figure": "Correlation matrix",
+            },
         ),
         normalized_counts="de_analysis/normalized_counts.csv",
         de_top_heatmap=report(
             "de_analysis/heatmap_top.svg",
             category="Results",
             caption="../report/heatmap_top.rst",
+            labels={
+                "figure": "Top gene heatmap",
+            },
         ),
         lfc_analysis="de_analysis/lfc_analysis.csv",
         volcano_plot=report(
             "de_analysis/volcano_plot.svg",
             category="Results",
             caption="../report/volcano_plot.rst",
+            labels={
+                "figure": "Volcano plot",
+            },
         ),
     params:
         samples=samples,

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -2,9 +2,7 @@ import os
 
 
 localrules:
-    compress_nplot,
-    compress_nplot_all,
-    compress_map_qc,
+    qm_report,
 
 
 configfile: "config/config.yml"
@@ -20,7 +18,12 @@ rule plot_samples:
         scatter=report(
             "NanoPlot/{sample}/NanoPlot-report.html",
             category="Quality control",
+            subcategory="NanoPlot",
             caption="../report/nanoplot_sample_report.rst",
+            labels={
+                "model": "NanoPlot",
+                "figure": "{sample}",
+            },
         ),
     params:
         outdir=lambda wildcards: f"NanoPlot/{wildcards.sample}",
@@ -42,7 +45,12 @@ rule plot_all_samples:
         scatter=report(
             "NanoPlot/all_samples/NanoPlot-report.html",
             category="Quality control",
+            subcategory="NanoPlot",
             caption="../report/nanoplot_all_samples_report.rst",
+            labels={
+                "model": "NanoPlot",
+                "figure": "All samples",
+            },
         ),
     # This parameter is in line with the Snakemake docs 8.20.3 guideline on how to avoid having parameters as output prefixes
     params:
@@ -56,32 +64,6 @@ rule plot_all_samples:
         "--fastq {input} --outdir {params.outdir} 2> {log}"
 
 
-rule compress_nplot:
-    input:
-        samples=rules.plot_samples.output,
-    output:
-        "QC/NanoPlot/{sample}.tar.gz",
-    log:
-        "logs/NanoPlot/compress_{sample}.log",
-    conda:
-        "../envs/base.yml"
-    script:
-        "../scripts/make_archive.py"
-
-
-rule compress_nplot_all:
-    input:
-        all_samples=rules.plot_all_samples.output,
-    output:
-        "QC/NanoPlot/all_samples.tar.gz",
-    log:
-        "logs/NanoPlot/compress_all_samples.log",
-    conda:
-        "../envs/base.yml"
-    script:
-        "../scripts/make_archive.py"
-
-
 rule map_qc:
     input:
         bam="sorted_alignments/{sample}_sorted.bam",
@@ -93,27 +75,37 @@ rule map_qc:
         "v4.4.0/bio/qualimap/bamqc"
 
 
-rule compress_map_qc:
+# this is a dummy rule to create input for the report because the QualiMap wrapper only accepts directories as valid output
+rule qm_report:
     input:
         map_qc=rules.map_qc.output,
     output:
-        "QC/qualimap/{sample}.tar.gz",
+        qm_report=report(
+            "qualimap/{sample}/qualimapReport.html",
+            category="Quality control",
+            subcategory="QualiMap",
+            caption="../report/qualimap.rst",
+            labels={
+                "model": "QualiMap",
+                "figure": "{sample}",
+            },
+        ),
     log:
-        "logs/qualimap/compress_{sample}.log",
+        "logs/qualimap/{sample}_report.log",
     conda:
         "../envs/base.yml"
-    script:
-        "../scripts/make_archive.py"
+    shell:
+        "cp -a QC/qualimap/{wildcards.sample} qualimap/ 2> {log}"
 
 
-rule sam_stats:
+rule bam_stats:
     input:
-        bam="sorted_alignments/{sample}.bam",
+        bam="alignments/{sample}.bam",
     output:
-        "QC/samstats/{sample}.txt",
+        "QC/bamstats/{sample}.txt",
     log:
-        "logs/samtools/samstats_{sample}.log",
+        "logs/samtools/bamstats_{sample}.log",
     params:
-        extra=f'{config["sstats_opts"]}',
+        extra=config["bamstats_opts"],
     wrapper:
         "v3.13.4/bio/samtools/stats"
diff --git a/workflow/rules/quantification.smk b/workflow/rules/quantification.smk
@@ -4,7 +4,7 @@ localrules:
 
 rule count_reads:
     input:
-        bam="sorted_alignments/{sample}.bam",
+        bam="alignments/{sample}.bam",
         trs="transcriptome/transcriptome.fa",
     output:
         tsv="counts/{sample}_salmon/quant.sf",