changelog

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 14.0.0
+current_version = 14.0.1
 commit = True
 tag = True
 tag_name = v{new_version}

BALSAMIC/__init__.py

@@ -1 +1 @@
-__version__ = "14.0.0"
+__version__ = "14.0.1"

BALSAMIC/__version__.py

@@ -1 +1 @@
-__version__ = "14.0.0"
+__version__ = "14.0.1"

BALSAMIC/snakemake_rules/pon/cnvkit_create_pon.rule

@@ -9,7 +9,7 @@ rule create_target:
         target_bed = cnv_dir + "target.bed",
         offtarget_bed = cnv_dir + "antitarget.bed"
     singularity:
-        Path(singularity_image, "varcall_cnvkit.sif").as_posix()
+        Path(singularity_image, "cnvkit.sif").as_posix()
     benchmark:
         Path(benchmark_dir, "cnvkit.targets.tsv").as_posix()
     shell:
@@ -27,7 +27,7 @@ rule create_coverage:
         target_cnn = cnv_dir + "{sample}.targetcoverage.cnn",
         antitarget_cnn = cnv_dir + "{sample}.antitargetcoverage.cnn"
     singularity:
-        Path(singularity_image, "varcall_cnvkit.sif").as_posix()
+        Path(singularity_image, "cnvkit.sif").as_posix()
     benchmark:
         Path(benchmark_dir, "cnvkit_{sample}.coverage.tsv").as_posix()
     shell:
@@ -43,7 +43,7 @@ rule create_reference:
     output:
         ref_cnn = pon_reference
     singularity:
-        Path(singularity_image, "varcall_cnvkit.sif").as_posix()
+        Path(singularity_image, "cnvkit.sif").as_posix()
     benchmark:
         Path(benchmark_dir, "cnvkit.reference.tsv").as_posix()
     shell:

BALSAMIC/snakemake_rules/variant_calling/somatic_cnv_tumor_normal_tga.rule

@@ -187,7 +187,12 @@ rule purecn_call_CNV_research:
         """
 export PURECN='/opt/PureCN/PureCN.R'
 
+
 # Run PureCN to estimate tumor-purity and ploidy
+
+# Keep exit_status to bypass bash stict mode and continue even if purecn fails.
+exit_status="true"
+{{
 Rscript $PURECN \
 --parallel \
 --out {params.tmpdir} \
@@ -200,32 +205,35 @@ Rscript $PURECN \
 --fun-segmentation Hclust \
 --force --post-optimize \
 --seed 124;
+}} || exit_status="false"
 
-if [[ -f "{params.tmpdir}/{params.sample_id}_dnacopy.seg" ]];  then
-mv {params.tmpdir}/{params.sample_id}_dnacopy.seg {params.cnv_csv};
-fi;
+if [ "$exit_status" = "true" ]; then
+    if [[ -f "{params.tmpdir}/{params.sample_id}_dnacopy.seg" ]];  then
+    mv {params.tmpdir}/{params.sample_id}_dnacopy.seg {params.cnv_csv};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}.pdf" ]];  then
-mv {params.tmpdir}/{params.sample_id}.pdf {params.purity_pdf};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}.pdf" ]];  then
+    mv {params.tmpdir}/{params.sample_id}.pdf {params.purity_pdf};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}_loh.csv" ]];  then
-mv {params.tmpdir}/{params.sample_id}_loh.csv {params.loh_regions};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}_loh.csv" ]];  then
+    mv {params.tmpdir}/{params.sample_id}_loh.csv {params.loh_regions};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}_genes.csv" ]];  then
-mv {params.tmpdir}/{params.sample_id}_genes.csv {params.loh_genes};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}_genes.csv" ]];  then
+    mv {params.tmpdir}/{params.sample_id}_genes.csv {params.loh_genes};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}.vcf.gz" ]];  then
-mv {params.tmpdir}/{params.sample_id}.vcf.gz {params.purecn_vcf};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}.vcf.gz" ]];  then
+    mv {params.tmpdir}/{params.sample_id}.vcf.gz {params.purecn_vcf};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}.csv" ]];  then
-mv {params.tmpdir}/{params.sample_id}.csv {output.purecn_purity};
+    if [[ -f "{params.tmpdir}/{params.sample_id}.csv" ]];  then
+    mv {params.tmpdir}/{params.sample_id}.csv {output.purecn_purity};
+    fi;
 else
 echo '"Sampleid","Purity","Ploidy","Sex","Contamination","Flagged","Failed","Curated","Comment"
-"tumor.initial",0.02,2,"?",0,FALSE,FALSE,FALSE,NA' > {output.purecn_purity}; 
+"tumor.initial",0.02,2,"?",0,FALSE,FALSE,FALSE,"FAILED PURITY ESTIMATION"' > {output.purecn_purity}; 
 fi;
 
 rm -rf {params.tmpdir};

BALSAMIC/snakemake_rules/variant_calling/somatic_cnv_tumor_only_tga.rule

@@ -126,6 +126,10 @@ rule purecn_call_CNV_research:
 export PURECN='/opt/PureCN/PureCN.R'
 
 # Run PureCN to estimate tumor-purity and ploidy
+
+# Keep exit_status to bypass bash stict mode and continue even if purecn fails.
+exit_status="true"
+{{
 Rscript $PURECN \
 --parallel \
 --out {params.tmpdir} \
@@ -138,32 +142,35 @@ Rscript $PURECN \
 --fun-segmentation Hclust \
 --force --post-optimize \
 --seed 124;
+}} || exit_status="false"
 
-if [[ -f "{params.tmpdir}/{params.sample_id}_dnacopy.seg" ]];  then
-mv {params.tmpdir}/{params.sample_id}_dnacopy.seg {params.cnv_csv};
-fi;
+if [ "$exit_status" = "true" ]; then
+    if [[ -f "{params.tmpdir}/{params.sample_id}_dnacopy.seg" ]];  then
+    mv {params.tmpdir}/{params.sample_id}_dnacopy.seg {params.cnv_csv};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}.pdf" ]];  then
-mv {params.tmpdir}/{params.sample_id}.pdf {params.purity_pdf};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}.pdf" ]];  then
+    mv {params.tmpdir}/{params.sample_id}.pdf {params.purity_pdf};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}_loh.csv" ]];  then
-mv {params.tmpdir}/{params.sample_id}_loh.csv {params.loh_regions};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}_loh.csv" ]];  then
+    mv {params.tmpdir}/{params.sample_id}_loh.csv {params.loh_regions};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}_genes.csv" ]];  then
-mv {params.tmpdir}/{params.sample_id}_genes.csv {params.loh_genes};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}_genes.csv" ]];  then
+    mv {params.tmpdir}/{params.sample_id}_genes.csv {params.loh_genes};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}.vcf.gz" ]];  then
-mv {params.tmpdir}/{params.sample_id}.vcf.gz {params.purecn_vcf};
-fi;
+    if [[ -f "{params.tmpdir}/{params.sample_id}.vcf.gz" ]];  then
+    mv {params.tmpdir}/{params.sample_id}.vcf.gz {params.purecn_vcf};
+    fi;
 
-if [[ -f "{params.tmpdir}/{params.sample_id}.csv" ]];  then
-mv {params.tmpdir}/{params.sample_id}.csv {output.purecn_purity};
+    if [[ -f "{params.tmpdir}/{params.sample_id}.csv" ]];  then
+    mv {params.tmpdir}/{params.sample_id}.csv {output.purecn_purity};
+    fi;
 else
 echo '"Sampleid","Purity","Ploidy","Sex","Contamination","Flagged","Failed","Curated","Comment"
-"tumor.initial",0.02,2,"?",0,FALSE,FALSE,FALSE,NA' > {output.purecn_purity};
+"tumor.initial",0.02,2,"?",0,FALSE,FALSE,FALSE,"FAILED PURITY ESTIMATION"' > {output.purecn_purity};
 fi;
 
 rm -rf {params.tmpdir};

CHANGELOG.rst

@@ -15,6 +15,14 @@ Removed:
 Fixed:
 ^^^^^^
 
+[14.0.1]
+-------
+
+Fixed:
+^^^^^^
+* PureCN fail due to bash strict mode https://github.com/Clinical-Genomics/BALSAMIC/pull/1406
+* Corrected name of CNVkit container in the CNVkit PON creation workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1412
+
 [14.0.0]
 -------
 
@@ -34,7 +42,6 @@ Fixed:
 * ASCAT-Ngs container https://github.com/Clinical-Genomics/BALSAMIC/pull/1395
 * bcftools in manta_tumor_normal uses correct column for tumor read filtering https://github.com/Clinical-Genomics/BALSAMIC/pull/1400
 
-
 [13.0.1]
 -------
 

CITATION.cff

@@ -18,5 +18,5 @@ authors:
 - family-names: "Wirta"
   given-names: "Valtteri"
 title: "BALSAMIC: Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer"
-version: v14.0.0
+version: v14.0.1
 url: "https://github.com/Clinical-Genomics/BALSAMIC"

README.rst

@@ -4,7 +4,7 @@
         <a href="https://github.com/Clinical-Genomics/BALSAMIC">
             <img  width=480 src="https://raw.githubusercontent.com/Clinical-Genomics/BALSAMIC/master/BALSAMIC/assets/images/balsamic_logo.png">
         </a>
-        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 14.0.0)</h3>
+        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 14.0.1)</h3>
         <h3 align="center">FastQ to Annotated VCF</h3>
     </p>
 
@@ -56,7 +56,7 @@ Snakemake cli given that there is a proper config file created.
 
 .. |docker_latest_build_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push.yml/badge.svg
 
-.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v14.0.0
+.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v14.0.1
 
 .. |snakemake_badge| image:: https://img.shields.io/badge/snakemake-%E2%89%A55.12.3-brightgreen.svg
 

docs/balsamic_methods.rst

@@ -5,7 +5,7 @@ Method description
 Target Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 14.0.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 14.0.1) was used to analyze the data from raw FASTQ files.
 We first quality controlled FASTQ files using FastQC v0.11.9 :superscript:`2`.
 Adapter sequences and low-quality bases were trimmed using fastp v0.23.2 :superscript:`3`.
 Trimmed reads were mapped to the reference genome hg19 using sentieon-tools 202010.02 :superscript:`15`.
@@ -26,7 +26,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
 Whole Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 14.0.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 14.0.1) was used to analyze the data from raw FASTQ files.
 We first quality controlled FASTQ files using FastQC v0.11.9 :superscript:`2`.
 Adapter sequences and low-quality bases were trimmed using fastp v0.23.2 :superscript:`3`.
 Trimmed reads were mapped to the reference genome hg19 using sentieon-tools 202010.02 :superscript:`15`.
@@ -46,7 +46,7 @@ to annotate somatic single nucleotide variants for their population allele frequ
 UMI Data Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 14.0.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 14.0.1) was used to analyze the data from raw FASTQ files.
 We first quality controlled FASTQ files using FastQC v0.11.9 :superscript:`2`.
 UMI tag extraction and consensus generation were performed using Sentieon tools v202010.02 :superscript:`15`.
 Adapter sequences and low-quality bases were trimmed using fastp v0.23.2 :superscript:`3`.

docs/bioinfo_softwares.rst

@@ -2,7 +2,7 @@
 Tools and software
 =================================
 
-BALSAMIC ( **version** = 14.0.0 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
+BALSAMIC ( **version** = 14.0.1 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
 one is included: usage and parameters, and relevant external links.
 
 ascatNgs

docs/install.rst

@@ -2,7 +2,7 @@
 Installation
 ============
 
-This section describes steps to install BALSAMIC (**version** = 14.0.0)
+This section describes steps to install BALSAMIC (**version** = 14.0.1)
 
 
 

docs/user_guide.rst

@@ -2,7 +2,7 @@
 Short tutorial
 ==============
 
-Here a short tutorial is provided for BALSAMIC (**version** = 14.0.0).
+Here a short tutorial is provided for BALSAMIC (**version** = 14.0.1).
 
 Regarding fastq-inputs
 ---------------------

setup.py

@@ -122,7 +122,7 @@
 
 setup(
     name=NAME,
-    version="14.0.0",
+    version="14.0.1",
     url=URL,
     author=AUTHOR,
     author_email=EMAIL,