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Dp24 spelling #45

Merged
merged 21 commits into from
Dec 10, 2024
Merged

Dp24 spelling #45

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111aa60
Updating
DLBPointon Dec 5, 2024
080321e
Updating modules
DLBPointon Dec 5, 2024
84817a6
Updating version to 1.1
DLBPointon Dec 5, 2024
28415b4
Merge branch 'dev' into dp24_spelling
DLBPointon Dec 5, 2024
4d72e53
Updating more
DLBPointon Dec 5, 2024
d406a12
prettier linting
DLBPointon Dec 5, 2024
058ed13
Updating setup from 1 to 2
DLBPointon Dec 5, 2024
1e0f35e
Adding tuple declaration
DLBPointon Dec 5, 2024
69fe17d
Replace generate_csv singularity container
DLBPointon Dec 6, 2024
8805be5
Updating testing
DLBPointon Dec 9, 2024
147b88f
Replace 0.0.2-yy5-c3 with 0.0.3-yy5-c1
DLBPointon Dec 9, 2024
0eb48b6
Remove anaconda ref in Utils and CITATIONS
DLBPointon Dec 9, 2024
4a1b70f
PRETTIER
DLBPointon Dec 9, 2024
84b1bce
Changing grep to actually get the version info
DLBPointon Dec 9, 2024
ff74ae3
Removing params
DLBPointon Dec 9, 2024
2764466
Changing version command, confirmed locally and in container
DLBPointon Dec 9, 2024
3c15e2d
Changin PERL version string and Updating executor values
DLBPointon Dec 9, 2024
9ad902d
Readding defaults
DLBPointon Dec 9, 2024
c6a2199
ONE SPACE caused version to not print
DLBPointon Dec 9, 2024
55756f1
Correct versioning information in modules
DLBPointon Dec 9, 2024
3d75460
Updating the changelog
DLBPointon Dec 9, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ jobs:
uses: actions/checkout@v3

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

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44 changes: 22 additions & 22 deletions modules.json
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Expand Up @@ -7,114 +7,114 @@
"nf-core": {
"bedtools/bamtobed": {
"branch": "master",
"git_sha": "1d1cb7bfef6cf67fbc7faafa6992ad8bdc3045b3",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bedtools/genomecov": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963",
"installed_by": ["modules"]
},
"bedtools/intersect": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bedtools/makewindows": {
"branch": "master",
"git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bedtools/map": {
"branch": "master",
"git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bedtools/merge": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bwamem2/index": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gnu/sort": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"minimap2/align": {
"branch": "master",
"git_sha": "efbf86bb487f288ac30660282709d9620dd6048e",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"minimap2/index": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"pretextmap": {
"branch": "master",
"git_sha": "6f4299292ef2c5b66e6829527b2647c301b77cc9",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/pretextmap/pretextmap.diff"
},
"pretextsnapshot": {
"branch": "master",
"git_sha": "b119603b5ebefa3075cfa513d1d91b1dc875a679",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/pretextsnapshot/pretextsnapshot.diff"
},
"samtools/faidx": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
},
"samtools/merge": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
"installed_by": ["modules"]
},
"samtools/view": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
"installed_by": ["modules"]
},
"seqtk/cutn": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"tabix/bgziptabix": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
"installed_by": ["modules"]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["modules"]
},
"windowmasker/mkcounts": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"windowmasker/ustat": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
}
}
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4 changes: 3 additions & 1 deletion modules/local/generate_cram_csv.nf
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Expand Up @@ -2,7 +2,9 @@ process GENERATE_CRAM_CSV {
tag "${meta.id}"
label 'process_single'

container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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2 changes: 0 additions & 2 deletions modules/nf-core/bedtools/bamtobed/environment.yml
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43 changes: 23 additions & 20 deletions modules/nf-core/bedtools/bamtobed/meta.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/bedtools/bamtobed/tests/main.nf.test
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2 changes: 0 additions & 2 deletions modules/nf-core/bedtools/genomecov/environment.yml
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13 changes: 10 additions & 3 deletions modules/nf-core/bedtools/genomecov/main.nf
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72 changes: 42 additions & 30 deletions modules/nf-core/bedtools/genomecov/meta.yml
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