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LaurenceKuhl authored Nov 11, 2024
2 parents c55bec1 + 6035a24 commit e37c4d1
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3 changes: 2 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -48,6 +48,7 @@ jobs:
profile: "conda"
- isMaster: false
profile: "singularity"
fail-fast: false # run all tests even if one fails

steps:
- name: Check out pipeline code
Expand Down Expand Up @@ -88,4 +89,4 @@ jobs:

- name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results_${{ matrix.test_name }}
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results_${{ matrix.test_name }}_${{ matrix.profile }}
15 changes: 14 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,15 @@
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).

## [v2.3.0 - Lime Nightingale](https://github.com/nf-core/crisprseq/releases/tag/2.3.0) - [16.10.2024]
## [v2.4.0dev]

### Added

### Fixed

### General

## [v2.3.0 - Lime Nightingale](https://github.com/nf-core/crisprseq/releases/tag/2.3.0) - [08.11.2024]

### Added

Expand All @@ -18,6 +26,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fix design matrix bug that introduced dots instead of a hyphen ([#190](https://github.com/nf-core/crisprseq/pull/190))
- Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty ([#190](https://github.com/nf-core/crisprseq/pull/190))
- Fix a typo in crisprcleanr/normalize, when a user inputs a file ([#192](https://github.com/nf-core/crisprseq/pull/192))
- Add Singularity and Docker tests in the CI, also fix any issues users had when running MAGeCKFlute with Docker or Singularity. ([#214](https://github.com/nf-core/crisprseq/pull/214))

### General

- Run pipeline tests with docker, singularity and conda on CI ([#185](https://github.com/nf-core/crisprseq/pull/185))

## [v2.2.1 Romarin Curie - patch](https://github.com/nf-core/crisprseq/releases/tag/2.2.1) - [23.07.2024]

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5 changes: 5 additions & 0 deletions README.md
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Expand Up @@ -104,6 +104,10 @@ nextflow run nf-core/crisprseq --input samplesheet.csv --analysis <targeted/scre
> [!WARNING]
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
> [!WARNING]
> Since Nextflow 23.07.0, Nextflow no longer mounts the host's HOME directory when using Apptainer or Singularity. MAGeCKFlute needs HOME directory write access. As a workaround, you can revert to the old behavior by setting the environment variable NXF_APPTAINER_HOME_MOUNT or NXF_SINGULARITY_HOME_MOUNT to true in the machine from which you launch the pipeline.
> `export NXF_SINGULARITY_HOME_MOUNT=true; nextflow run nf-core/crisprseq --input samplesheet.csv --analysis screening --outdir <OUTDIR> -profile <singularity/aptainer>`
For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/crisprseq/usage) and the [parameter documentation](https://nf-co.re/crisprseq/parameters).

## Pipeline output
Expand Down Expand Up @@ -132,6 +136,7 @@ We thank the following people for their extensive assistance in the development
- [@jianhong](https://github.com/jianhong)
- [@joannakraw](https://github.com/joannakraw)
- [@mashehu](https://github.com/mashehu)
- [@medmaca](https://github.com/medmaca)
- [@metinyazar](https://github.com/metinyazar)
- [@msanvicente](https://github.com/msanvicente)
- [@mschaffer-incyte](https://github.com/mschaffer-incyte)
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,8 +1,8 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/crisprseq/releases/tag/2.3.0" target="_blank">nf-core/crisprseq</a>
This report has been generated by the <a href="https://github.com/nf-core/crisprseq/tree/dev" target="_blank">nf-core/crisprseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/crisprseq/2.3.0/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/crisprseq/dev/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-crisprseq-methods-description":
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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -317,7 +317,7 @@ process {
}

withName: MEDAKA {
ext.args = '-m r941_min_high_g303'
ext.args = { "-m ${model}" }
ext.prefix = { "${reads.baseName}_medakaConsensus" }
}

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3 changes: 2 additions & 1 deletion modules.json
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Expand Up @@ -95,7 +95,8 @@
"racon": {
"branch": "master",
"git_sha": "f5ed3ac0834b68e80a00a06a61d04ce8e896f275",
"installed_by": ["modules"]
"installed_by": ["modules"],
"patch": "modules/nf-core/racon/racon.diff"
},
"samtools/index": {
"branch": "master",
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2 changes: 1 addition & 1 deletion modules/local/hitselection.nf
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Expand Up @@ -2,7 +2,7 @@ process HITSELECTION {
tag "${meta.treatment}_${meta.reference}"
label 'process_high'

conda "r-base=4.4.1,r-igraph=2.0.3,r-dplyr=1.1.4,r-tidyr=1.3.1,r-readr=2.1.5,r-ggplot2=3.5.1"
conda "r-base=4.4.1 r-igraph=2.0.3 r-dplyr=1.1.4 r-tidyr=1.3.1 r-readr=2.1.5 r-ggplot2=3.5.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-dcfb6eba6adda57b9d4a990b9096cb040320914f:588e2c290fce5c5c11ef2340b6184370efd2c628-0':
'biocontainers/mulled-v2-dcfb6eba6adda57b9d4a990b9096cb040320914f:588e2c290fce5c5c11ef2340b6184370efd2c628-0' }"
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6 changes: 3 additions & 3 deletions modules/local/mageck/flutemle.nf
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Expand Up @@ -3,10 +3,10 @@ process MAGECK_FLUTEMLE {
tag "$prefix"
label 'process_high'

conda "bioconda::bioconductor-mageckflute=2.2.0"
conda "bioconda::bioconductor-mageckflute==2.6.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.2.0--r42hdfd78af_0':
'biocontainers/bioconductor-mageckflute:2.2.0--r42hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.6.0--r43hdfd78af_0':
'biocontainers/bioconductor-mageckflute:2.6.0--r43hdfd78af_0' }"

input:
tuple val(meta), path(gene_summary)
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11 changes: 4 additions & 7 deletions modules/local/mageck/graphrra.nf
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Expand Up @@ -2,10 +2,10 @@ process MAGECK_GRAPHRRA {
tag "$meta.treatment"
label 'process_single'

conda "bioconda::bioconductor-mageckflute=2.2.0"
conda "bioconda::bioconductor-mageckflute==2.6.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mageckflute:2.2.0--r42hdfd78af_0':
'biocontainers/bioconductor-mageckflute:2.2.0--r42hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.6.0--r43hdfd78af_0':
'biocontainers/bioconductor-mageckflute:2.6.0--r43hdfd78af_0' }"

input:
tuple val(meta), path(gene_summary)
Expand All @@ -27,11 +27,10 @@ process MAGECK_GRAPHRRA {
#### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text.
####
#### Orient a reference sequence according to reads orientation.
Sys.setenv(HOME = getwd()) # Required for Singularity/Apptainer
library(MAGeCKFlute)
library(ggplot2)
options(ggrepel.max.overlaps = Inf)
gdata = ReadRRA("$gene_summary")
gdata <- transform(gdata, LogFDR = -log10(FDR))
png(filename = paste0("$meta.treatment","_vs_","$meta.reference","_scatterview.png"), width = 6, height = 4, units = "in", res = 300)
Expand Down Expand Up @@ -60,6 +59,4 @@ process MAGECK_GRAPHRRA {
writeLines(version_ggplot, f)
close(f)
"""


}
2 changes: 1 addition & 1 deletion modules/local/matricescreation.nf
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@@ -1,7 +1,7 @@
process MATRICESCREATION {
label 'process_single'

conda 'r-ggplot2=3.4.3 bioconductor-shortread=1.58.0 r-ggpubr=0.6.0 r-ggmsa=1.0.2 r-seqmagick=0.1.6 r-tidyr=1.3.0 r-ggseqlogo=0.1 r-cowplot=1.1.1 r-seqinr=4.2_30 r-optparse=1.7.3 r-dplyr=1.1.2 r-plyr=1.8.8 r-stringr=1.5.0 r-plotly=4.10.2'
conda 'conda-forge::r-base==4.0'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-6de07928379e6eface08a0019c4a1d6b5192e805:0d77388f37ddd923a087f7792e30e83ab54c918c-0' :
'biocontainers/mulled-v2-6de07928379e6eface08a0019c4a1d6b5192e805:0d77388f37ddd923a087f7792e30e83ab54c918c-0' }"
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3 changes: 2 additions & 1 deletion modules/local/orient_reference.nf
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Expand Up @@ -2,7 +2,8 @@ process ORIENT_REFERENCE {
tag "$meta.id"
label 'process_single'

conda "r-seqinr=4.2_16 bioconductor-biostrings=2.62.0 bioconductor-shortread=1.52.0"
// jpeg is required in the conda container to fix a "libjpeg.so.9: No such file or directory" error
conda "r-seqinr=4.2_16 bioconductor-biostrings=2.62.0 bioconductor-shortread=1.52.0 jpeg=9d"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-63136bce0d642de81864be727b6b42a26026e33b:d3ce5caf7bcbf6cecedcf51b0135646831c01e77-0' :
'biocontainers/mulled-v2-63136bce0d642de81864be727b6b42a26026e33b:d3ce5caf7bcbf6cecedcf51b0135646831c01e77-0' }"
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2 changes: 1 addition & 1 deletion modules/local/venndiagram.nf
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Expand Up @@ -3,7 +3,7 @@ process VENNDIAGRAM {
label 'process_low'


conda "bioconda::r-venndiagram=1.6.16"
conda "conda-forge::r-ggvenn=0.1.10"
container "ghcr.io/qbic-pipelines/rnadeseq:dev"

input:
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/medaka/environment.yml

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5 changes: 3 additions & 2 deletions modules/nf-core/medaka/main.nf

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9 changes: 9 additions & 0 deletions modules/nf-core/medaka/medaka.diff

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12 changes: 6 additions & 6 deletions modules/nf-core/racon/main.nf

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32 changes: 32 additions & 0 deletions modules/nf-core/racon/racon.diff

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30 changes: 15 additions & 15 deletions modules/nf-core/vsearch/cluster/main.nf

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51 changes: 50 additions & 1 deletion modules/nf-core/vsearch/cluster/vsearch-cluster.diff

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