Add bookmarks in variant calling result

LUMC · Mar 5, 2024 · 8dcd9b9 · 8dcd9b9
2 parents d86481b + 7246607
commit 8dcd9b9
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,12 +8,15 @@ Changelog
 .. that users understand how the changes affect the new version.
 
 **********
-v2.0.5-dev
+v2.0.6-dev
 **********
+* Update FastQC to 0.12.1
 * Modified PDF formatting
   -Add bookmarks under chapter variant
   -Sort the genes of interest alphabetically
   -Lock snakefmt version
+* Sort the genes of interest alphabetically
+
 **********
 v2.0.5
 **********

diff --git a/includes/qc-seq/Snakefile b/includes/qc-seq/Snakefile
@@ -45,9 +45,7 @@ rule fastqc_raw:
     output:
         folder=directory("{sample}/qc-seq/{read_group}/fastqc-{pair}-raw"),
     params:
-        xms="4096M",
-        xmx="4096M",
-        fastqc_dir="usr/local/opt/fastqc-0.11.9",
+        memory=4096,
     log:
         "log/fastqc_raw.{sample}.{read_group}.{pair}.txt",
     threads: 4
@@ -57,16 +55,13 @@ rule fastqc_raw:
         """
         mkdir -p {output.folder}
 
-        FASTQC_DIR=/{params.fastqc_dir}
-        export CLASSPATH="$FASTQC_DIR:$FASTQC_DIR/sam-1.103.jar:$FASTQC_DIR/jbzip2-0.9.jar:$FASTQC_DIR/cisd-jhdf5.jar"
-
-        java -Djava.awt.headless=true -Xms{params.xms} -Xmx{params.xmx} \
-            -Dfastqc.output_dir={output.folder} \
-            -Dfastqc.io.tmpdir={input.tmp} \
-            -Dfastqc.unzip=true \
-            -Dfastqc.nogroup=true \
-            -Dfastqc.threads={threads} \
-            uk.ac.babraham.FastQC.FastQCApplication \
+        fastqc \
+            --outdir {output.folder} \
+            --dir {input.tmp} \
+            --extract \
+            --nogroup \
+            --threads {threads} \
+            --memory {params.memory} \
             {input.fq1:q} {input.fq2:q} 2> {log}
         """
 
@@ -102,39 +97,15 @@ rule cutadapt:
         """
 
 
-rule fastqc_processed:
-    """Runs FastQC for each pair of QC-ed inputs."""
+use rule fastqc_raw as fastqc_processed with:
     input:
         fq1="{sample}/qc-seq/{read_group}/{sample}-{read_group}-R1.fq.gz",
         fq2="{sample}/qc-seq/{read_group}/{sample}-{read_group}-R2.fq.gz",
         tmp="tmp",
     output:
         folder=directory("{sample}/qc-seq/{read_group}/fastqc-{pair}-processed"),
-    params:
-        xms="4096M",
-        xmx="4096M",
-        fastqc_dir="usr/local/opt/fastqc-0.11.9",
     log:
         "log/fastqc_processed.{sample}.{read_group}.{pair}.txt",
-    threads: 4
-    container:
-        containers["fastqc"]
-    shell:
-        """
-        mkdir -p {output.folder}
-
-        FASTQC_DIR=/{params.fastqc_dir}
-        export CLASSPATH="$FASTQC_DIR:$FASTQC_DIR/sam-1.103.jar:$FASTQC_DIR/jbzip2-0.9.jar:$FASTQC_DIR/cisd-jhdf5.jar"
-
-        java -Djava.awt.headless=true -Xms{params.xms} -Xmx{params.xmx} \
-            -Dfastqc.output_dir={output.folder} \
-            -Dfastqc.io.tmpdir={input.tmp} \
-            -Dfastqc.unzip=true \
-            -Dfastqc.nogroup=true \
-            -Dfastqc.threads={threads} \
-            uk.ac.babraham.FastQC.FastQCApplication \
-            {input.fq1:q} {input.fq2:q} 2> {log}
-        """
 
 
 rule rg_stats:

diff --git a/includes/qc-seq/common.smk b/includes/qc-seq/common.smk
@@ -4,7 +4,7 @@ from types import SimpleNamespace
 containers = {
     "crimson": "docker://quay.io/biocontainers/crimson:1.1.0--pyh5e36f6f_0",
     "cutadapt": "docker://quay.io/biocontainers/cutadapt:4.1--py310h1425a21_1",
-    "fastqc": "docker://quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1",
+    "fastqc": "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0",
 }
 
 

diff --git a/report/templates/contents_var.html.j2 b/report/templates/contents_var.html.j2
@@ -3,7 +3,6 @@
 
 <h1>Variant Calling Results</h1>
 
-
 {% set vars = {'figure_idx': 1, 'table_idx': 10} %}
 {% for gene in stats.cov %}
   {% for tid, exons in stats.cov[gene].items() %}

diff --git a/test/helper.sh b/test/helper.sh
@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+set -euxo pipefail
+
+ref=test/data/reference/hamlet-ref.fa
+star=test/data/reference/hamlet-star/Genome
+
+function setup {
+  unxz -k ${ref}.xz
+  unxz -k ${star}.xz
+}
+
+function cleanup {
+  rm -f ${ref}
+  rm -f ${star}
+}
+
+trap cleanup EXIT
+
+setup
diff --git a/test/test_fusion.yml b/test/test_fusion.yml
@@ -48,7 +48,7 @@
     - fusion
   command: >
     bash -c "
-    unxz -k test/data/reference/hamlet-ref.fa.xz;
+    source test/helper.sh
 
     snakemake -rp
     --snakefile includes/fusion/Snakefile
@@ -60,8 +60,6 @@
     --use-singularity
     --singularity-args '--cleanenv --bind /tmp'
     --singularity-prefix '~/.singularity/cache/snakemake'
-
-    rm test/data/reference/hamlet-ref.fa;
     "
   files:
     # Should create the arriba output files

diff --git a/test/test_hamlet.yml b/test/test_hamlet.yml
@@ -58,10 +58,7 @@
     - hamlet
   command: >
     bash -c "
-    set -e 
-
-    unxz -k test/data/reference/hamlet-ref.fa.xz;
-    unxz -k test/data/reference/hamlet-star/Genome.xz;
+    source test/helper.sh
 
     snakemake -rp \
       --snakefile Snakefile \
@@ -72,9 +69,6 @@
       --use-singularity \
       --singularity-args '--cleanenv --bind /tmp' \
       --singularity-prefix '~/.singularity/cache/snakemake'
-
-    rm test/data/reference/hamlet-ref.fa;
-    rm test/data/reference/hamlet-star/Genome;
     "
     - path: MO1-RNAseq-1-16714/hamlet_report.SRR8615409.pdf
     - path: "log/generate_report.MO1-RNAseq-1-16714.txt"
@@ -86,26 +80,20 @@
     - hamlet
   command: >
     bash -c "
-    set -e 
-
-    unxz -k test/data/reference/hamlet-ref.fa.xz;
-    unxz -k test/data/reference/hamlet-star/Genome.xz;
+    source test/helper.sh
 
     snakemake \
       --snakefile Snakefile \
       --configfile test/data/config/hamlet.json \
       --config pepfile=test/pep/chrM_itd.csv \
-      --cores \
+      --cores 1 \
       --verbose \
       --use-singularity \
       --singularity-args '--cleanenv --bind /tmp' \
       --singularity-prefix '~/.singularity/cache/snakemake' \
       SRR8615409/hamlet_report.SRR8615409.html \
       SRR8615409/hamlet_report.SRR8615409.pdf
 
-    rm test/data/reference/hamlet-ref.fa;
-    rm test/data/reference/hamlet-star/Genome;
-
     # Test if the table scripts can still parse the summary.json file
     
     python3 utilities/hamlet_table.py variant SRR8615409/SRR8615409.summary.json > variant.tsv;

diff --git a/test/test_qc_seq.yml b/test/test_qc_seq.yml
@@ -50,9 +50,9 @@
 
     contains_regex:
     # The forward/reverse fastq files from the PEP should be handled correctly
-    - '-Dfastqc.output_dir=TestSample1.* test/data/fastq/R1.fq.gz test/data/fastq/R2.fq.gz'
-    - '-Dfastqc.output_dir=TestSample2.* test/data/fastq/R1.fq.gz test/data/fastq/R2.fq.gz'
-    - "-Dfastqc.output_dir=TestSample2.* 'test/data/fastq/SRR8615409 chrM_1.fastq.gz' 'test/data/fastq/SRR8615409 chrM_2.fastq.gz'"
+    - 'fastqc .* --outdir TestSample1.* test/data/fastq/R1.fq.gz test/data/fastq/R2.fq.gz'
+    - 'fastqc .* --outdir TestSample2.* test/data/fastq/R1.fq.gz test/data/fastq/R2.fq.gz'
+    - "fastqc .* --outdir TestSample2.* 'test/data/fastq/SRR8615409 chrM_1.fastq.gz' 'test/data/fastq/SRR8615409 chrM_2.fastq.gz'"
 
 # Singularity should be available
 - name: test-qc-sanity-singularity

diff --git a/test/test_report.py b/test/test_report.py
@@ -32,10 +32,6 @@ def parse_table(table):
     # Get the rows
     for row in table.find("tbody").find_all("tr"):
         d = {k: v.get_text() for k, v in zip(headers, row.find_all("td"))}
-        # Convert the price field to float
-        # for k, v in d.items():
-        #     if "€" in v:
-        #         d[k] = price_to_float(v)
         data.append(d)
     return data
 

diff --git a/test/test_snv_indels.yml b/test/test_snv_indels.yml
@@ -46,8 +46,7 @@
     - snv-indels
   command: >
     bash -c "
-    unxz -k test/data/reference/hamlet-ref.fa.xz;
-    unxz -k test/data/reference/hamlet-star/Genome.xz;
+    source test/helper.sh
 
     snakemake -rp \
       --snakefile includes/snv-indels/Snakefile \
@@ -59,9 +58,6 @@
       --use-singularity \
       --singularity-args '--cleanenv --bind /tmp' \
       --singularity-prefix '~/.singularity/cache/snakemake'
-
-    rm test/data/reference/hamlet-ref.fa;
-    rm test/data/reference/hamlet-star/Genome;
     "
   stderr:
     # snv-indel should not use a local VEP database, but query ensembl