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feat: release 9.0.0 #902

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merged 71 commits into from
May 3, 2022
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53cbf69
add interval bed option to umi TNscope
Dec 13, 2021
e4eddba
add tests
Dec 13, 2021
ac11689
update changelog
Dec 13, 2021
2f8a50a
fix black
Dec 13, 2021
1b81a73
update padding to 100
Dec 13, 2021
9f68b5e
Merge pull request #837 from Clinical-Genomics/fix/umi_intervalbed
ashwini06 Dec 17, 2021
456e4d8
Merge branch 'master' into develop
Dec 20, 2021
7b4148e
feat: generate canfam3 references (#843)
rannick Dec 22, 2021
233d7bc
refactor: merge QC metric extraction workflows (#833)
ivadym Dec 23, 2021
a581951
add umi dups metrics to multiqc
Jan 4, 2022
8d0c896
remove wrong spacing for comments
Jan 4, 2022
c5c9726
add changelog
Jan 4, 2022
016f579
remove fastp exclusion
Jan 11, 2022
12128b7
update changelog
Jan 11, 2022
4ee2ba2
#845 from Clinical-Genomics/feat/umi_duprate
ashwini06 Jan 13, 2022
4e29a32
fix: capture kit empty argument for WGS runs (#850)
ivadym Jan 24, 2022
b4cda37
fix: QC panel bed version generalisation (#855)
ivadym Feb 7, 2022
95685ab
Merge branch 'master' into develop
Feb 9, 2022
c7b6924
merge master changes to develop
Feb 16, 2022
15964ab
add vcf2cytosure container
Feb 24, 2022
75b6def
add vcf2cytosure container tests
Feb 24, 2022
7b9dfbb
update changelog
Feb 24, 2022
a3daf44
add newlines
Feb 24, 2022
03ba91d
add vcf2cytosure to git actions
Feb 28, 2022
42dd1ab
change alpine version
Feb 28, 2022
ded392a
remove previous pip install vcf2cytosure
Feb 28, 2022
1d03303
fix label key in dockerfile
Feb 28, 2022
f7decab
test balsamic container image to updated version
Feb 28, 2022
e4e242e
remove vcf2cytosure from annotate tests
Mar 1, 2022
1eb5f60
test invalide label key
Mar 1, 2022
2fed80c
test invalide label key
Mar 1, 2022
abea014
fix invalid label key
Mar 1, 2022
18b61ea
remove --no-cache-dir from pip dockerfile
Mar 1, 2022
70fbdbe
update changelog
Mar 2, 2022
5c3d5b5
add vcf2cytosure to commons
Mar 2, 2022
7933a91
fix black linter
Mar 2, 2022
8c2b2af
feat: add SVDB (#872)
khurrammaqbool Mar 3, 2022
c0404be
fix pythonpath
Mar 4, 2022
0c6ee47
fix conflicts
Mar 4, 2022
89b5e69
Merge pull request #869 from Clinical-Genomics/feat/add_vcf2cytosure
ashwini06 Mar 7, 2022
1451d11
feat: add svdb workflow (#873)
khurrammaqbool Mar 8, 2022
e1eeb00
feat: add svdb workflow tga (#879)
khurrammaqbool Mar 9, 2022
f286961
merge changes from master
Mar 9, 2022
e017773
feat: create cgh files from cnvkit outputs (#880)
ashwini06 Mar 14, 2022
c749a3c
feat: svdb merge sv cnv (#886)
khurrammaqbool Mar 15, 2022
59ed2fd
feat: remove sv and cnv callers from annotation and filter rules (#889)
khurrammaqbool Mar 16, 2022
8914b31
feat: remove vcfanno and cosmic for sv (#891)
khurrammaqbool Mar 28, 2022
cd97dbd
fix: update svdb to 2.6.0 (#901)
khurrammaqbool Apr 4, 2022
bd70c3a
feat: Option to use PON with TGA cnvkit (#851)
ashwini06 Apr 4, 2022
a80860c
merge master changes to develop
Apr 4, 2022
998e68c
update changelog
Apr 4, 2022
cb10e60
refactor: redundant files and varaibles from balsamic (#903)
ashwini06 Apr 6, 2022
f366976
update changelog and correct it
Apr 6, 2022
b27c519
feat: extract additional WGS QC metrics (#907)
ivadym Apr 11, 2022
cf98015
merge master changes to develop
Apr 12, 2022
096df69
fix: remove stat files and add count files for scout upload VCFs (#899)
khurrammaqbool Apr 13, 2022
580f4e2
docs: balsamic methods description in readthedocs (#906)
ashwini06 Apr 19, 2022
b272c95
feat: add ascatngs copynumber (#914)
khurrammaqbool Apr 19, 2022
e8385cd
refactor: remove QC delivery report wokflow (#913)
ivadym Apr 19, 2022
f50afa5
Merge branch 'develop' into release/9_0_0
Apr 19, 2022
9ea3dcf
feat: add qc only workflow (#847)
rannick Apr 20, 2022
74e5475
docs: add annotation resources (#916)
khurrammaqbool Apr 20, 2022
cb8e5b6
feat: update delly (#920)
khurrammaqbool Apr 22, 2022
4e2bdd7
fix: Change of gnomad pop freq value for UMI workflow (#919)
ashwini06 Apr 26, 2022
23773a5
feat: add Delly CNV for tumor only workflow (#923)
khurrammaqbool Apr 27, 2022
782e721
feat: add delly CNV read-depth profile (#924)
khurrammaqbool Apr 28, 2022
91aeda9
refactor: Remove gatk haplotypcaller (#922)
ashwini06 Apr 29, 2022
8142fac
refactor: balsamic containers (#921)
ashwini06 May 2, 2022
5120e17
refactor: Update the list of files to be stored and delivered (#915)
ivadym May 2, 2022
e628c42
feat: bcftools counts QC validation (#925)
ivadym May 2, 2022
a376a1f
Merge branch 'develop' into release/9_0_0
May 2, 2022
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8 changes: 7 additions & 1 deletion BALSAMIC/snakemake_rules/quality_control/multiqc.rule
Original file line number Diff line number Diff line change
@@ -58,6 +58,7 @@ else:

if config["umiworkflow"]:
multiqc_input.extend(expand(umi_qc_dir + "{sample}.umi.collect_hsmetric", sample=config["samples"]))
multiqc_input.extend(expand(umi_qc_dir + "{sample}.umi.metrics", sample=config["samples"]))


rule multiqc:
@@ -81,7 +82,12 @@ rule multiqc:
shell:
"""
echo -e \"{params.dir_list}\" > {params.qc_dir}/dir_list;
multiqc --force --outdir {params.qc_dir} --exclude {params.exclude_module} --data-format json -l {params.qc_dir}/dir_list;

multiqc --force --outdir {params.qc_dir} \
--exclude {params.exclude_module} \
--data-format json \
-l {params.qc_dir}/dir_list;

chmod -R 777 {params.qc_dir};
"""

8 changes: 2 additions & 6 deletions BALSAMIC/snakemake_rules/umi/qc_umi.rule
Original file line number Diff line number Diff line change
@@ -2,8 +2,6 @@
# coding: utf-8

## UmiAwareMarkDuplicatesWithMateCigar - umimetrics


rule picard_umiaware:
input:
bam = umi_dir + "{sample}_consensusfiltered_umi.bam"
@@ -29,9 +27,8 @@ O={output.bam} \
M={output.duplicates} \
UMI_METRICS={output.umimetrics};
"""
## CollectHSmetrics - median target coverage-required


## CollectHSmetrics - median target coverage-required
rule picard_collecthsmetrics_umi:
input:
bam = umi_dir + "{sample}_consensusfiltered_umi.bam",
@@ -68,9 +65,8 @@ COVERAGE_CAP=50000 \
BAIT_SET_NAME={params.baitsetname} \
METRIC_ACCUMULATION_LEVEL=ALL_READS;
"""
## SUM(Reads in each family)/ the number of families after correction, collapsing on supporting reads.


## SUM(Reads in each family)/ the number of families after correction, collapsing on supporting reads.
rule samtools_view_calculatemeanfamilydepth_umi:
input:
bam = umi_dir + "{sample}_consensusfiltered_umi.bam"
1 change: 1 addition & 0 deletions CHANGELOG.rst
Original file line number Diff line number Diff line change
@@ -6,6 +6,7 @@ Added:

* Snakemake workflow to create canfam3 reference #843
* Call umi variants using TNscope in bed defined regions #821
* UMI duplication metrics to report in multiqc_picard_dups.json #844

Changed:
^^^^^^^^