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Merge pull request #205 from planemo-autoupdate/workflows/epigenetics…
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Updating workflows/epigenetics/hic-hicup-cooler from 0.2.1 to 0.3
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@mvdbeek
mvdbeek authored Sep 15, 2023
2 parents ea2c65f + 7f525af commit 0689b57
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18 changes: 9 additions & 9 deletions workflows/epigenetics/hic-hicup-cooler/.dockstore.yml
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Expand Up @@ -3,36 +3,36 @@ workflows:
- name: hic-fastq-to-cool-hicup-cooler
subclass: Galaxy
publish: true
primaryDescriptorPath: /hic_fastq_to_cool_hicup_cooler.ga
primaryDescriptorPath: /hic-fastq-to-cool-hicup-cooler.ga
testParameterFiles:
- /hic_fastq_to_cool_hicup_cooler-tests.yml
- /hic-fastq-to-cool-hicup-cooler-tests.yml
authors:
- name: Lucille Delisle
orcid: 0000-0002-1964-4960
- name: chic-fastq-to-cool-hicup-cooler
subclass: Galaxy
publish: true
primaryDescriptorPath: /chic_fastq_to_cool_hicup_cooler.ga
primaryDescriptorPath: /chic-fastq-to-cool-hicup-cooler.ga
testParameterFiles:
- /chic_fastq_to_cool_hicup_cooler-tests.yml
- /chic-fastq-to-cool-hicup-cooler-tests.yml
authors:
- name: Lucille Delisle
orcid: 0000-0002-1964-4960
- name: hic-juicermediumtabix-to_cool-cooler
- name: hic-juicermediumtabix-to-cool-cooler
subclass: Galaxy
publish: true
primaryDescriptorPath: /hic_juicermediumtabix_to_cool_cooler.ga
primaryDescriptorPath: /hic-juicermediumtabix-to-cool-cooler.ga
testParameterFiles:
- /hic_juicermediumtabix_to_cool_cooler-tests.yml
- /hic-juicermediumtabix-to-cool-cooler-tests.yml
authors:
- name: Lucille Delisle
orcid: 0000-0002-1964-4960
- name: hic-fastq-to-pairs-hicup
subclass: Galaxy
publish: true
primaryDescriptorPath: /hic_fastq_to_pairs_hicup.ga
primaryDescriptorPath: /hic-fastq-to-pairs-hicup.ga
testParameterFiles:
- /hic_fastq_to_pairs_hicup-tests.yml
- /hic-fastq-to-pairs-hicup-tests.yml
authors:
- name: Lucille Delisle
orcid: 0000-0002-1964-4960
6 changes: 6 additions & 0 deletions workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md
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@@ -1,5 +1,11 @@
# Changelog

## [0.3] 2023-09-08

### Update tools
- all cooler tools were updated from 0.8.11 to 0.9.3
- pyGenomeTracks was updated from 3.7 to 3.8

## [0.2.1] 2023-09-01 Bug fix

Fix dockstore (workflows are the same)
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0 ...chic_fastq_to_cool_hicup_cooler-tests.yml → ...chic-fastq-to-cool-hicup-cooler-tests.yml
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82 changes: 41 additions & 41 deletions ...cooler/chic_fastq_to_cool_hicup_cooler.ga → ...cooler/chic-fastq-to-cool-hicup-cooler.ga
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Expand Up @@ -10,7 +10,7 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.2.1",
"release": "0.3",
"name": "cHi-C_fastqToCool_hicup_cooler",
"steps": {
"0": {
Expand Down Expand Up @@ -319,7 +319,7 @@
"outputs": [],
"position": {
"left": 520,
"top": 0.0
"top": 0
},
"subworkflow": {
"a_galaxy_workflow": "true",
Expand Down Expand Up @@ -741,23 +741,13 @@
}
},
"tags": "",
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Expand All @@ -767,6 +757,16 @@
"label": "valid pairs in juicebox format MAPQ filtered",
"output_name": "valid pairs in juicebox format MAPQ filtered",
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Expand Down Expand Up @@ -933,7 +933,7 @@
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Expand Down Expand Up @@ -975,15 +975,15 @@
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Expand Down Expand Up @@ -1170,7 +1170,7 @@
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Expand Down Expand Up @@ -1203,23 +1203,23 @@
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Expand Down Expand Up @@ -1258,15 +1258,15 @@
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Expand All @@ -1280,7 +1280,7 @@
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Expand Down Expand Up @@ -1320,15 +1320,15 @@
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Expand All @@ -1342,28 +1342,28 @@
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Expand Down Expand Up @@ -1398,15 +1398,15 @@
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Expand All @@ -1422,6 +1422,6 @@
"tags": [
"Hi-C"
],
"uuid": "f310abac-4a50-41fa-a59a-84c51816a462",
"version": 1
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4 changes: 2 additions & 2 deletions .../hic_fastq_to_cool_hicup_cooler-tests.yml → .../hic-fastq-to-cool-hicup-cooler-tests.yml
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Expand Up @@ -21,7 +21,7 @@
No fill-in: 'false'
minimum MAPQ: 30
Bin size in bp: 1000000
Interactions to consider to calculate weights in normalization step: --cis-only
Interactions to consider to calculate weights in normalization step: ""
region for matrix plotting: chr2:175,689,620-178,604,461
outputs:
HiCUP report (html):
Expand Down Expand Up @@ -76,7 +76,7 @@
test_dataset:
asserts:
has_size:
value: 123613
value: 149349
delta: 10000
plot with pyGenomeTracks:
class: File
Expand Down
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