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fix: linting for github actions #56

Merged
merged 63 commits into from
Aug 15, 2024
Merged

fix: linting for github actions #56

merged 63 commits into from
Aug 15, 2024

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yeising
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@yeising yeising commented Aug 6, 2024

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yeising and others added 30 commits August 6, 2024 11:04
@yeising
fix: linting for github actions
69e6d9d
@yeising
fix: renamed sample to match validator pattern
3028949
@yeising
fix: path for inputdir
58c48bf
@yeising
fix: provided directory for github action Linting
944f1d9
@cmeesters
fix: linting of path composition
804d6c1
@cmeesters
fix: output is no parameter anymore
f41ea29
@cmeesters
fix: fix of fix for commons - wrong brace order, missing brace
6dc6a8a
@yeising
fix: added missing conda envs to remaining rules
e45ea04
@yeising
fix: added logs and a script for info
710bf94
@yeising
fix: relocated localrule declaration to appropriate file
3b9c82c
@cmeesters
fix: simplified suffix expansion and fixed linter hiccup
377ae1d
@yeising
fix: added missing conda env to rule merge_counts
a9765f8
@cmeesters
fix: gnarf - forgotten closing brace
ef0b0fe
@yeising
fix: removed unnecessary rule write coldata, added logs to rules, add…
90dda12 
…ed conda envs to rules, created script for write_de_params
@yeising
Merge branch 'fix-lint-gitaction' of https://github.com/snakemake-wor…
87b7328 
…kflows/transcriptome-differential-expression into fix-lint-gitaction
@cmeesters
fix: deleted localrules which do not exist in this file
06e9676
@cmeesters
Merge branch 'fix-lint-gitaction' of github.com:snakemake-workflows/t…
b26dcc7 
…ranscriptome-differential-expression into fix-lint-gitaction
@yeising
fix: added localrules to correct file
f22062e
@cmeesters
Update issue templates (#57)
5444215
@cmeesters
Update issue templates (#59)
f08e4c1
@yeising
style: formatting
bf96301
@yeising
style: formatting
aa4579d
@yeising
style: formatting
169220e
@yeising
fix: get_mapped_reads_input function now returns sample path with ext…
f3ff222 
…ension
@yeising
style: formatting
3c55b1b
@yeising
ci: updated super-linter
ebaa78e
@yeising
ci: downgraded super-linter to v4 again
4ea12b0
@yeising
refactor: removed optional sequencing summary input for NanoPlot read qc
99a149a
@yeising
chore: updated snakemake
7d30585
@yeising
fix: restored sample_QC input for rule_all,+ snakefmt
99acf01
cmeesters and others added 22 commits August 15, 2024 09:42
@cmeesters @yeising
fix: fix of fix for commons - wrong brace order, missing brace
c60753d
@cmeesters @yeising
fix: simplified suffix expansion and fixed linter hiccup
a0d9742
@cmeesters @yeising
fix: gnarf - forgotten closing brace
4067265
@cmeesters @yeising
fix: deleted localrules which do not exist in this file
8498a2c
@yeising
fix: added missing conda envs to remaining rules
f4841e5
@yeising
fix: added logs and a script for info
a4aa1d2
@yeising
fix: relocated localrule declaration to appropriate file
920c9c8
@yeising
fix: added missing conda env to rule merge_counts
b0ccf90
@yeising
fix: removed unnecessary rule write coldata, added logs to rules, add…
48a9009 
…ed conda envs to rules, created script for write_de_params
@yeising
fix: added localrules to correct file
cbf0926
@yeising
style: formatting
92b4338
@yeising
style: formatting
76cccba
@yeising
style: formatting
4d77572
@yeising
fix: get_mapped_reads_input function now returns sample path with ext…
954bd47 
…ension
@yeising
ci: updated super-linter
eb9f15a
@yeising
ci: downgraded super-linter to v4 again
615f70c
@yeising
refactor: removed optional sequencing summary input for NanoPlot read qc
02cf71c
@yeising
chore: updated snakemake
357ce85
@yeising
fix: restored sample_QC input for rule_all,+ snakefmt
37c37d1
@yeising
refactor: removed redundant rule all input variable sample_QC
0e553a7
@yeising
Merge branch 'fix-lint-gitaction' of https://github.com/snakemake-wor…
887972f 
…kflows/transcriptome-differential-expression into fix-lint-gitaction
@yeising
style: formatting
ada1ca1
yeising
yeising commented Aug 15, 2024
View reviewed changes
workflow/rules/commons.smk Outdated
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Deals with #30 .

@cmeesters
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one step further, no successful testing, yet - need to have download rules for references.

@cmeesters cmeesters merged commit 54605ae into main Aug 15, 2024
4 of 5 checks passed
@cmeesters cmeesters deleted the fix-lint-gitaction branch August 15, 2024 12:13
This was referenced Aug 15, 2024
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@cmeesters cmeesters cmeesters approved these changes

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@yeising @cmeesters