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nf-core_modules/modules/homer/makeucscfile/meta.yml

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Homer Modules (#75) * feat(homer): Add initial makeTagDirectory * feat(homer): Add initial findPeaks module * feat(homer): Update with new options See 1d30e2c21affedc742680e8e04d60c6481d9cd11 * fix(homer): Correct findpeaks process name * fix(homer): Takes a bam file instead of bed * feat(homer): Add initial makeTagDirectory test * fix(homer): Hardcode genome and configureHomer I'd like to modularize configureHomer, but I need to figure out how exactly the genomes work. * fix(homer): bam => bed Bam requires samtools to be present, which it's not in this docker image * feat(homer): Add initial configureHomer script * ci(homer): Add initial test * test(homer): Reproducible configuration workaround - I can't run both tests(one file and two files) at the same time because it breaks - I can't copy the genome stuff from the configurehomer module because it's read only - So I can't make the makeTagDirectory module depend on configureHomer * test(homer): Add placeholder annotatepeaks The required inputs are necessarily required for all workflows from what I've used, but I'll need to look at the actual docs * test(homer): Add missing B.bed * test(homer): Rename two => groseq Then all of the various workflows that homer provides can be e2e tested * feat(homer): Add initial makeUCSCfile module * test(homer): Add start to makeUCSCfile testing * chore(homer): Add various cleanups * test(homer): Rewrite annotatepeaks Not passing yet * test(homer): Rewrite configurehomer * test(homer): Rewrite findpeaks Still failing * test(homer): Rewrite makeucscfile Not passing yet * test(homer): Rewrite maketagdirectory All homer modules now follow the new structure. Time to make them pass. * test(homer): Fix typo for workflow name * fix(homer): Use correct container * fix(homer): Accept fasta in maketagdirectory Apparently all of the homer stuff can just take any old fasta and you don't need to configure the genome ahead of time with configureHomer * test(homer): makeTagDirectory passes now * fix(homer): Update containers in makeucscfile * test(homer): Rewrite makeucscfile Takes input from maketagdirectory which is how the module should be used * fix(homer): Update makeUCSCFile bedgraph path * test(homer): Update makeucscfile expected output * fix(homer): Update containers in findpeaks * fix(homer): Change findpeaks args The user is just going to have to know what they're doing for now * test(homer): findPeaks rewrite with tagDir input * test(homer): Update expected files for findPeaks And bump filters * style: Appease editorconfig * ci: Remove old workflow * tests(homer): Add md5sums * test(homer): Add meta test * style(homer): Capitalize HOMER * docs(homer): Add maketagdirectory meta.yml * docs(homer): Add makeucscfile meta.yml * docs(homer): Add findpeaks meta.yml * test(homer): Update to new test data standards * chore: Remove stuff that got revived in the rebase * chore: software => modules * test(homer): Update tags * test(homer): Update annotatepeaks * ci: Fix uploading of artifacts GitHub actions doesn't like the / in the tags * test(homer): Remove annotate md5sum This is failing and breaking new tests * test(homer): Use bams instead of beds * test(homer): Fix meta maketagdirectory * test(homer): Fix input in all tests * test(homer): Move back to bed files Forgot samtools isn't present * chore(homer): Add TODOs for tests * test(homer): Add bed format arg * test(homer): Update md5sums * test(homer): Fix tags tsvs * style(homer): Appease nf-core linting * docs(homer): Be in line with what is in the main.nf file Co-authored-by: Kevin Menden <kevin.menden@live.com> Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
name: homer_makeucscfile
description: Create a UCSC bed graph with the HOMER suite
keywords:
- peaks
- bed
- bedGraph
tools:
- homer:
description: |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
documentation: http://homer.ucsd.edu/homer/
doi: 10.1016/j.molcel.2010.05.004.
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
licence: ["GPL-3.0-or-later"]
Homer Modules (#75) * feat(homer): Add initial makeTagDirectory * feat(homer): Add initial findPeaks module * feat(homer): Update with new options See 1d30e2c21affedc742680e8e04d60c6481d9cd11 * fix(homer): Correct findpeaks process name * fix(homer): Takes a bam file instead of bed * feat(homer): Add initial makeTagDirectory test * fix(homer): Hardcode genome and configureHomer I'd like to modularize configureHomer, but I need to figure out how exactly the genomes work. * fix(homer): bam => bed Bam requires samtools to be present, which it's not in this docker image * feat(homer): Add initial configureHomer script * ci(homer): Add initial test * test(homer): Reproducible configuration workaround - I can't run both tests(one file and two files) at the same time because it breaks - I can't copy the genome stuff from the configurehomer module because it's read only - So I can't make the makeTagDirectory module depend on configureHomer * test(homer): Add placeholder annotatepeaks The required inputs are necessarily required for all workflows from what I've used, but I'll need to look at the actual docs * test(homer): Add missing B.bed * test(homer): Rename two => groseq Then all of the various workflows that homer provides can be e2e tested * feat(homer): Add initial makeUCSCfile module * test(homer): Add start to makeUCSCfile testing * chore(homer): Add various cleanups * test(homer): Rewrite annotatepeaks Not passing yet * test(homer): Rewrite configurehomer * test(homer): Rewrite findpeaks Still failing * test(homer): Rewrite makeucscfile Not passing yet * test(homer): Rewrite maketagdirectory All homer modules now follow the new structure. Time to make them pass. * test(homer): Fix typo for workflow name * fix(homer): Use correct container * fix(homer): Accept fasta in maketagdirectory Apparently all of the homer stuff can just take any old fasta and you don't need to configure the genome ahead of time with configureHomer * test(homer): makeTagDirectory passes now * fix(homer): Update containers in makeucscfile * test(homer): Rewrite makeucscfile Takes input from maketagdirectory which is how the module should be used * fix(homer): Update makeUCSCFile bedgraph path * test(homer): Update makeucscfile expected output * fix(homer): Update containers in findpeaks * fix(homer): Change findpeaks args The user is just going to have to know what they're doing for now * test(homer): findPeaks rewrite with tagDir input * test(homer): Update expected files for findPeaks And bump filters * style: Appease editorconfig * ci: Remove old workflow * tests(homer): Add md5sums * test(homer): Add meta test * style(homer): Capitalize HOMER * docs(homer): Add maketagdirectory meta.yml * docs(homer): Add makeucscfile meta.yml * docs(homer): Add findpeaks meta.yml * test(homer): Update to new test data standards * chore: Remove stuff that got revived in the rebase * chore: software => modules * test(homer): Update tags * test(homer): Update annotatepeaks * ci: Fix uploading of artifacts GitHub actions doesn't like the / in the tags * test(homer): Remove annotate md5sum This is failing and breaking new tests * test(homer): Use bams instead of beds * test(homer): Fix meta maketagdirectory * test(homer): Fix input in all tests * test(homer): Move back to bed files Forgot samtools isn't present * chore(homer): Add TODOs for tests * test(homer): Add bed format arg * test(homer): Update md5sums * test(homer): Fix tags tsvs * style(homer): Appease nf-core linting * docs(homer): Be in line with what is in the main.nf file Co-authored-by: Kevin Menden <kevin.menden@live.com> Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- tagDir:
type: directory
description: "The 'Tag Directory'"
pattern: "tagDir"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bedGraph:
type: file
description: The UCSC bed graph
pattern: "tag_dir/*ucsc.bedGraph.gz"
Update versions key in meta.yml for all modules (#787)
2021-10-03 07:20:26 +00:00
- versions:
Homer Modules (#75) * feat(homer): Add initial makeTagDirectory * feat(homer): Add initial findPeaks module * feat(homer): Update with new options See 1d30e2c21affedc742680e8e04d60c6481d9cd11 * fix(homer): Correct findpeaks process name * fix(homer): Takes a bam file instead of bed * feat(homer): Add initial makeTagDirectory test * fix(homer): Hardcode genome and configureHomer I'd like to modularize configureHomer, but I need to figure out how exactly the genomes work. * fix(homer): bam => bed Bam requires samtools to be present, which it's not in this docker image * feat(homer): Add initial configureHomer script * ci(homer): Add initial test * test(homer): Reproducible configuration workaround - I can't run both tests(one file and two files) at the same time because it breaks - I can't copy the genome stuff from the configurehomer module because it's read only - So I can't make the makeTagDirectory module depend on configureHomer * test(homer): Add placeholder annotatepeaks The required inputs are necessarily required for all workflows from what I've used, but I'll need to look at the actual docs * test(homer): Add missing B.bed * test(homer): Rename two => groseq Then all of the various workflows that homer provides can be e2e tested * feat(homer): Add initial makeUCSCfile module * test(homer): Add start to makeUCSCfile testing * chore(homer): Add various cleanups * test(homer): Rewrite annotatepeaks Not passing yet * test(homer): Rewrite configurehomer * test(homer): Rewrite findpeaks Still failing * test(homer): Rewrite makeucscfile Not passing yet * test(homer): Rewrite maketagdirectory All homer modules now follow the new structure. Time to make them pass. * test(homer): Fix typo for workflow name * fix(homer): Use correct container * fix(homer): Accept fasta in maketagdirectory Apparently all of the homer stuff can just take any old fasta and you don't need to configure the genome ahead of time with configureHomer * test(homer): makeTagDirectory passes now * fix(homer): Update containers in makeucscfile * test(homer): Rewrite makeucscfile Takes input from maketagdirectory which is how the module should be used * fix(homer): Update makeUCSCFile bedgraph path * test(homer): Update makeucscfile expected output * fix(homer): Update containers in findpeaks * fix(homer): Change findpeaks args The user is just going to have to know what they're doing for now * test(homer): findPeaks rewrite with tagDir input * test(homer): Update expected files for findPeaks And bump filters * style: Appease editorconfig * ci: Remove old workflow * tests(homer): Add md5sums * test(homer): Add meta test * style(homer): Capitalize HOMER * docs(homer): Add maketagdirectory meta.yml * docs(homer): Add makeucscfile meta.yml * docs(homer): Add findpeaks meta.yml * test(homer): Update to new test data standards * chore: Remove stuff that got revived in the rebase * chore: software => modules * test(homer): Update tags * test(homer): Update annotatepeaks * ci: Fix uploading of artifacts GitHub actions doesn't like the / in the tags * test(homer): Remove annotate md5sum This is failing and breaking new tests * test(homer): Use bams instead of beds * test(homer): Fix meta maketagdirectory * test(homer): Fix input in all tests * test(homer): Move back to bed files Forgot samtools isn't present * chore(homer): Add TODOs for tests * test(homer): Add bed format arg * test(homer): Update md5sums * test(homer): Fix tags tsvs * style(homer): Appease nf-core linting * docs(homer): Be in line with what is in the main.nf file Co-authored-by: Kevin Menden <kevin.menden@live.com> Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
type: file
Update versions key in meta.yml for all modules (#787)
2021-10-03 07:20:26 +00:00
description: File containing software versions
Bulk update modules to use versions.yml (#739) * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 08:41:24 +00:00
pattern: "versions.yml"
Homer Modules (#75) * feat(homer): Add initial makeTagDirectory * feat(homer): Add initial findPeaks module * feat(homer): Update with new options See 1d30e2c21affedc742680e8e04d60c6481d9cd11 * fix(homer): Correct findpeaks process name * fix(homer): Takes a bam file instead of bed * feat(homer): Add initial makeTagDirectory test * fix(homer): Hardcode genome and configureHomer I'd like to modularize configureHomer, but I need to figure out how exactly the genomes work. * fix(homer): bam => bed Bam requires samtools to be present, which it's not in this docker image * feat(homer): Add initial configureHomer script * ci(homer): Add initial test * test(homer): Reproducible configuration workaround - I can't run both tests(one file and two files) at the same time because it breaks - I can't copy the genome stuff from the configurehomer module because it's read only - So I can't make the makeTagDirectory module depend on configureHomer * test(homer): Add placeholder annotatepeaks The required inputs are necessarily required for all workflows from what I've used, but I'll need to look at the actual docs * test(homer): Add missing B.bed * test(homer): Rename two => groseq Then all of the various workflows that homer provides can be e2e tested * feat(homer): Add initial makeUCSCfile module * test(homer): Add start to makeUCSCfile testing * chore(homer): Add various cleanups * test(homer): Rewrite annotatepeaks Not passing yet * test(homer): Rewrite configurehomer * test(homer): Rewrite findpeaks Still failing * test(homer): Rewrite makeucscfile Not passing yet * test(homer): Rewrite maketagdirectory All homer modules now follow the new structure. Time to make them pass. * test(homer): Fix typo for workflow name * fix(homer): Use correct container * fix(homer): Accept fasta in maketagdirectory Apparently all of the homer stuff can just take any old fasta and you don't need to configure the genome ahead of time with configureHomer * test(homer): makeTagDirectory passes now * fix(homer): Update containers in makeucscfile * test(homer): Rewrite makeucscfile Takes input from maketagdirectory which is how the module should be used * fix(homer): Update makeUCSCFile bedgraph path * test(homer): Update makeucscfile expected output * fix(homer): Update containers in findpeaks * fix(homer): Change findpeaks args The user is just going to have to know what they're doing for now * test(homer): findPeaks rewrite with tagDir input * test(homer): Update expected files for findPeaks And bump filters * style: Appease editorconfig * ci: Remove old workflow * tests(homer): Add md5sums * test(homer): Add meta test * style(homer): Capitalize HOMER * docs(homer): Add maketagdirectory meta.yml * docs(homer): Add makeucscfile meta.yml * docs(homer): Add findpeaks meta.yml * test(homer): Update to new test data standards * chore: Remove stuff that got revived in the rebase * chore: software => modules * test(homer): Update tags * test(homer): Update annotatepeaks * ci: Fix uploading of artifacts GitHub actions doesn't like the / in the tags * test(homer): Remove annotate md5sum This is failing and breaking new tests * test(homer): Use bams instead of beds * test(homer): Fix meta maketagdirectory * test(homer): Fix input in all tests * test(homer): Move back to bed files Forgot samtools isn't present * chore(homer): Add TODOs for tests * test(homer): Add bed format arg * test(homer): Update md5sums * test(homer): Fix tags tsvs * style(homer): Appease nf-core linting * docs(homer): Be in line with what is in the main.nf file Co-authored-by: Kevin Menden <kevin.menden@live.com> Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
authors:
- "@EMiller88"
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