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fix: processing vembrane config #330

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merged 9 commits into from
Oct 17, 2024
Merged

fix: processing vembrane config #330

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e2a1e55
fix: processing vembrane config
FelixMoelder Oct 2, 2024
6fcf048
fix linting
FelixMoelder Oct 2, 2024
9c9e688
fix formatting
FelixMoelder Oct 9, 2024
683e62b
linting
FelixMoelder Oct 14, 2024
3714872
linting
FelixMoelder Oct 14, 2024
a886c2b
Merge branch 'master' into fix/vembrane_config
FelixMoelder Oct 14, 2024
7269264
parse exon as raw
FelixMoelder Oct 17, 2024
54cc7e9
fmt
FelixMoelder Oct 17, 2024
0deaf0d
reset wrappers
FelixMoelder Oct 17, 2024
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2 changes: 1 addition & 1 deletion workflow/rules/candidate_calling.smk
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Expand Up @@ -20,7 +20,7 @@ rule freebayes:
),
threads: max(workflow.cores - 1, 1) # use all available cores -1 (because of the pipe) for calling
wrapper:
"v2.7.0/bio/freebayes"
"v4.4.0/bio/freebayes"
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Is this necessary for anything (like a bug fix in a newer version of freebayes or the wrapper)? Because otherwise I would leave this as is, so as not to trigger rerunning of the candidate calling in workflows that update to a newer release after merging this PR...



rule delly:
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10 changes: 6 additions & 4 deletions workflow/rules/common.smk
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Expand Up @@ -1169,10 +1169,12 @@ def get_vembrane_config(wildcards, input):

def append_items(items, renames, field_func, header_func=None):
for item in items:
if item in renames:
header_name = renames[item]["name"]
if "expr" in renames[item]:
parts_field = renames[item]["expr"]
if type(item) == dict or item in renames:
entry = item if type(item) == dict else renames[item]
header_name = entry["name"]
if "expr" in entry:
parts_field = entry["expr"]
# TODO How can this case be covered in the config file?
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else:
parts_field = field_func(item)
else:
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2 changes: 1 addition & 1 deletion workflow/rules/mapping.smk
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Expand Up @@ -83,7 +83,7 @@ rule mark_duplicates:
#https://broadinstitute.github.io/picard/faq.html
mem_mb=3000,
wrapper:
"v2.5.0/bio/picard/markduplicates"
"v4.2.0/bio/picard/markduplicates"
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As above: if such an update is not really necessary for anything in this pull request, I would defer updating to whenever this is really necessary. Otherwise this will trigger reruns in previously workflows where we update to a newer workflow version...



rule calc_consensus_reads:
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2 changes: 1 addition & 1 deletion workflow/rules/plugins.smk
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Expand Up @@ -6,7 +6,7 @@ rule download_revel:
conda:
"../envs/curl.yaml"
shell:
"curl https://rothsj06.dmz.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip -o {output} &> {log}"
"curl https://zenodo.org/records/7072866/files/revel-v1.3_all_chromosomes.zip -o {output} &> {log}"
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Nice, let's hope this stays more robust in the long-term and that newer versions will also end up on Zenodo!



rule process_revel_scores:
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