Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Release prep #103

Merged
merged 13 commits into from
Jan 21, 2023
Merged

Release prep #103

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
3585458
chore: Add missing DOI
edmundmiller Jan 20, 2023
fdde946
chore: Clean up neglected CHANGELOG
edmundmiller Jan 20, 2023
66f1d86
chore: Update modules
edmundmiller Jan 21, 2023
a2674e0
fix: Update FASTP Inputs
edmundmiller Jan 21, 2023
c0b3bdf
fix: Update index channels
edmundmiller Jan 21, 2023
2cadc48
fix: Update bedtools sort inputs
edmundmiller Jan 21, 2023
0da6267
chore: Remove unused test config hack
edmundmiller Jan 21, 2023
4f0467a
fix: Remove all enable_conda calls
edmundmiller Jan 21, 2023
b98cdc2
fix: Roll back dragmap align
edmundmiller Jan 21, 2023
bc2e0f4
chore: Bump snapshot after module updates
edmundmiller Jan 21, 2023
8692d83
chore: Update CHANGELOG
edmundmiller Jan 21, 2023
2c83809
chore: Add missing descriptions
edmundmiller Jan 21, 2023
8bfc348
chore: Bump version
edmundmiller Jan 20, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
16 changes: 8 additions & 8 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,22 +3,22 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## Unreleased
## v2.1.0 - 2023-01-20

### Added

- Added a second BEDTools intersect step to allow filtering and overlapping in the same workflow.
- [[#94](https://github.com/nf-core/nascent/pull/94)] - Added a second BEDTools intersect step to allow filtering and overlapping in the same workflow.
- [[#101](https://github.com/nf-core/nascent/pull/101)] - Initialized nf-test

### Changed

### Fixed

- Updated PINTS version from 1.1.6 to 1.1.8 ([Fixes an issue where PINTS fails if one of the predictions was empty](https://github.com/hyulab/PINTS/issues/12))
- Add HOMER channels to fix error about "Missing workflow output parameter: homer_peaks" when homer is skipped
- [[#103](https://github.com/nf-core/nascent/pull/103)] - Updated Modules

### Deprecated
### Fixed

### Removed
- [[841ae62](https://github.com/nf-core/nascent/commit/841ae62)] - Updated PINTS version from 1.1.6 to 1.1.8 ([Fixes an issue where PINTS fails if one of the predictions was empty](https://github.com/hyulab/PINTS/issues/12))
- [[#97](https://github.com/nf-core/nascent/pull/97)] - Add HOMER channels to fix error about "Missing workflow output parameter: homer_peaks" when homer is skipped
- Add missing DOIs

## v2.0.0 - 2022-10-24

Expand Down
5 changes: 2 additions & 3 deletions lib/WorkflowMain.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,8 @@ class WorkflowMain {
//
public static String citation(workflow) {
return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
// TODO nf-core: Add Zenodo DOI for pipeline after first release
//"* The pipeline\n" +
//" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
"* The pipeline\n" +
" https://doi.org/10.5281/zenodo.7245273\n\n" +
"* The nf-core framework\n" +
" https://doi.org/10.1038/s41587-020-0439-x\n\n" +
"* Software dependencies\n" +
Expand Down
83 changes: 42 additions & 41 deletions modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,87 +7,88 @@
"nf-core": {
"bbmap/pileup": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"bedtools/genomecov": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"bedtools/intersect": {
"branch": "master",
"git_sha": "4bb1d4e362a38642e877afe41aaf58ded9e56c86",
"git_sha": "e576ba52f6babb06cd7946c286e5bb4f494ee02c",
"installed_by": ["modules"]
},
"bedtools/merge": {
"branch": "master",
"git_sha": "4bb1d4e362a38642e877afe41aaf58ded9e56c86",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"bedtools/sort": {
"branch": "master",
"git_sha": "4bb1d4e362a38642e877afe41aaf58ded9e56c86",
"git_sha": "f1f473b21811b958d1317c4a97c56e16d3ee40f9",
"installed_by": ["modules"]
},
"bwa/index": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"bwa/mem": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"bwamem2/index": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"bwamem2/mem": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"cat/cat": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"deeptools/bamcoverage": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"dragmap/align": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules"]
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"],
"patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
},
"dragmap/hashtable": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"fastqc": {
Expand All @@ -97,112 +98,112 @@
},
"gffread": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"homer/findpeaks": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["homer/groseq"]
},
"homer/maketagdirectory": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["homer/groseq"]
},
"homer/makeucscfile": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["homer/groseq"]
},
"homer/pos2bed": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["homer/groseq"]
},
"multiqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
"installed_by": ["modules"]
},
"pints/caller": {
"branch": "master",
"git_sha": "a8c6d338a76df3736215c93c27d9ccc7b88e9cf4",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"preseq/ccurve": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"rseqc/inferexperiment": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"rseqc/readdistribution": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"rseqc/readduplication": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_sort_stats_samtools", "bam_dedup_stats_samtools_umitools"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_stats_samtools"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
"untar": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
}
}
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bed2saf.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process BED2SAF {
tag "$meta.id"
label 'process_single'

conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
Expand Down
2 changes: 1 addition & 1 deletion modules/local/grohmm/parametertuning/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process GROHMM_PARAMETERTUNING {
label 'process_high'
label 'process_long'

conda (params.enable_conda ? "conda-forge::r-base=4.1.1 conda-forge::r-optparse=1.7.1 conda-forge::r-argparse=2.1.3 bioconda::bioconductor-genomicfeatures=1.46.1 bioconda::bioconductor-grohmm=1.28.0" : null)
conda "conda-forge::r-base=4.1.1 conda-forge::r-optparse=1.7.1 conda-forge::r-argparse=2.1.3 bioconda::bioconductor-genomicfeatures=1.46.1 bioconda::bioconductor-grohmm=1.28.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-e9a6cb7894dd2753aff7d9446ea95c962cce8c46:0a46dae3241b1c4f02e46468f5d54eadcf64beca-0' :
'quay.io/biocontainers/mulled-v2-e9a6cb7894dd2753aff7d9446ea95c962cce8c46:0a46dae3241b1c4f02e46468f5d54eadcf64beca-0' }"
Expand Down
2 changes: 1 addition & 1 deletion modules/local/grohmm/transcriptcalling/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process GROHMM_TRANSCRIPTCALLING {
label 'process_high'
label 'process_long'

conda (params.enable_conda ? "conda-forge::r-base=4.1.1 conda-forge::r-optparse=1.7.1 conda-forge::r-argparse=2.1.3 bioconda::bioconductor-genomicfeatures=1.46.1 bioconda::bioconductor-grohmm=1.28.0" : null)
conda "conda-forge::r-base=4.1.1 conda-forge::r-optparse=1.7.1 conda-forge::r-argparse=2.1.3 bioconda::bioconductor-genomicfeatures=1.46.1 bioconda::bioconductor-grohmm=1.28.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-e9a6cb7894dd2753aff7d9446ea95c962cce8c46:0a46dae3241b1c4f02e46468f5d54eadcf64beca-0' :
'quay.io/biocontainers/mulled-v2-e9a6cb7894dd2753aff7d9446ea95c962cce8c46:0a46dae3241b1c4f02e46468f5d54eadcf64beca-0' }"
Expand Down
2 changes: 1 addition & 1 deletion modules/local/gtf2bed.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process GTF2BED {
tag "$gtf"
label 'process_low'

conda (params.enable_conda ? "conda-forge::perl=5.26.2" : null)
conda "conda-forge::perl=5.26.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
'quay.io/biocontainers/perl:5.26.2' }"
Expand Down
2 changes: 1 addition & 1 deletion modules/local/gtf_gene_filter.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process GTF_GENE_FILTER {
tag "$fasta"
label 'process_low'

conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
'quay.io/biocontainers/python:3.8.3' }"
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/bbmap/pileup/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/bedtools/genomecov/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.