ChIP-seq and ATAC-seq mutliple comparisons

[katsikora]

• fixes #947

[NixBio]

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Katarzyna Sikora @.***> 5.1.24 13:48 >>>

• fixes #947 You can view, comment on, or merge this pull request online at:

  https://github.com/maxplanck-ie/snakepipes/pull/959

-- Commit Summary --

• csaw multicomp
• CSAW multicomp wip
• fix ChIP snakefile
• fix ATAC-seq snakefile
• fix ATAC-seq internals
• ChIPseq multiComp CI tests
• dag test
• dag test
• dag test
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• does this work
• does this work
• does this work
• Merge pull request #957 from maxplanck-ie/develop
• does this work
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• dag test
• conditional warning
• dag test
• test
• does this work
• fix for no controls
• fix all samples
• various fixes chipseq wo control
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• fix test dag
• fix test dag
• fix csaw snakefile
• csaw multicomp
• csaw multicomp
• does this work
• does this work
• does this work
• does this work
• nearestGene
• fix
• chipseq snakefile
• fixes chipseq snakefile
• does this work
• fix snakefile
• csaw multicomp
• fix
• test dag
• wildcards compGroup
• fixes reordered dict
• does this work
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• does this work
• fix cf
• fix
• fix
• does this work
• fix
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• fix
• fix
• genrich
• fix Snakefile
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• fix
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• does this wotk
• test
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• cleanup
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• test
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• cleanup
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• test
• test
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• cleanup print statement
• dag test
• test dag
• test dag
• test dag
• Genrich spikein
• test dag
• test dag
• test dag
• test dag
• cleanup print statement
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• fix rMats
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• dag test
• dag test
• dag test
• dag test
• dag test
• dag test
• dag test
• dag test
• dag test
• dag test
• dag test
• dag test
• fix atacseq
• fix atacseq
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• test dag
• flake
• fix flake
• 9 samples and chipdict
• added tests to pytest
• pytest and news
• dna mapping and partial chipseq
• chipdict nocontrol
• chipdict nocontrol
• pytest
• does this work
• try to fix Genrich test failing
• does this work
• does this work
• does this work
• does this work
• genrich fix
• pytest fixes
• atac-seq ci
• fixes atacseq
• run CSAW
• test dag
• atacseq genrich
• fix genrich snakefile
• fix genrich snakefile
• test dag
• test dag
• test dag
• test dag
• broad config ci
• test dag
• test dag
• pytest broad and atac multicomp
• pytest
• fixes pytest

-- File Changes --

A .ci_stuff/ChIP.sample_broad_config.yaml (19)
M .ci_stuff/ChIP.sample_config.yaml (14)
A .ci_stuff/ChIP.sample_noControl_config.yaml (19)
A .ci_stuff/ChIP.sample_short_config.yaml (13)
M .ci_stuff/test_dag.sh (231)
M .gitignore (3)
M docs/content/News.rst (4)
M snakePipes/common_functions.py (28)
M snakePipes/shared/rules/ATAC.snakefile (42)
A snakePipes/shared/rules/CSAW.multiComp.snakefile (224)
R snakePipes/shared/rules/CSAW.singleComp.snakefile (87)
M snakePipes/shared/rules/ChIP_peak_calling.snakefile (105)
M snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile (112)
M snakePipes/shared/rules/deepTools_ChIP.snakefile (4)
A snakePipes/shared/rules/nearestGene.multiComp.snakefile (34)
R snakePipes/shared/rules/nearestGene.singleComp.snakefile (0)
M snakePipes/shared/rules/rMats.multipleComp.snakefile (2)
M snakePipes/shared/rules/rMats.singleComp.snakefile (2)
M snakePipes/workflows/ATAC-seq/Snakefile (34)
M snakePipes/workflows/ATAC-seq/internals.snakefile (14)
M snakePipes/workflows/ChIP-seq/Snakefile (76)
M snakePipes/workflows/ChIP-seq/internals.snakefile (33)
M tests/test_jobcounts.py (594)

-- Patch Links --

https://github.com/maxplanck-ie/snakepipes/pull/959.patch https://github.com/maxplanck-ie/snakepipes/pull/959.diff

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