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

Update container #47

Merged
merged 4 commits into from
Aug 11, 2023
Merged

Update container #47

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
6f92a4d
update mulled container
christopher-mohr Aug 10, 2023
5de6f52
update CHANGELOG
christopher-mohr Aug 10, 2023
399cee0
update container, conda string
christopher-mohr Aug 11, 2023
89a72cd
update CHANGELOG
christopher-mohr Aug 11, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 7 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#46](https://github.com/nf-core/nanostring/pull/46) - Publish NACHO QC reports [#44](https://github.com/nf-core/nanostring/issues/44)
- [#46](https://github.com/nf-core/nanostring/pull/46) - Publish `NACHO` QC reports [#44](https://github.com/nf-core/nanostring/issues/44)
- [#47](https://github.com/nf-core/nanostring/pull/47) - Update `NACHO` R package including bug fix [#45](https://github.com/nf-core/nanostring/issues/45)
- [#48](https://github.com/nf-core/nanostring/pull/48) - Set correct `conda` environment for `COMPUTE_GENE_SCORES` process

### `Dependencies`

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `nacho` | 2.0.4 | 2.0.5 |

### `Deprecated`

## v1.1.1 - 2023-06-23
Expand Down
2 changes: 1 addition & 1 deletion modules/local/compute_gene_scores.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process COMPUTE_GENE_SCORES {
label 'process_single'

conda "r-nacho=2.0.4 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
conda "r-yaml=2.3.7 r-ggplot2=3.4.2 r-tidylog=1.0.2 r-tidyverse=2.0.0 r-stringr=1.5.0 bioconductor-gsva=1.46.0 bioconductor-singscore=1.18.0 r-factominer=2.8.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
grst marked this conversation as resolved.
Show resolved Hide resolved
'https://depot.galaxyproject.org/singularity/mulled-v2-dfd42984f8ba1b1d0d13648f30430581dff51e82:2a27d1707e91426237b882a7ba5adec8724f9069-0' :
'biocontainers/mulled-v2-dfd42984f8ba1b1d0d13648f30430581dff51e82:2a27d1707e91426237b882a7ba5adec8724f9069-0' }"
Expand Down
6 changes: 3 additions & 3 deletions modules/local/create_annotated_tables.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
process CREATE_ANNOTATED_TABLES {
label 'process_single'

conda "r-nacho=2.0.4 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
conda "r-nacho=2.0.5 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' }"

input:
path counts
Expand Down
6 changes: 3 additions & 3 deletions modules/local/create_gene_heatmap.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
process CREATE_GENE_HEATMAP {
label 'process_single'

conda "r-nacho=2.0.4 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
conda "r-nacho=2.0.5 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' }"

input:
path annotated_counts
Expand Down
6 changes: 3 additions & 3 deletions modules/local/nacho/normalize.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
process NACHO_NORMALIZE {
label 'process_single'

conda "r-nacho=2.0.4 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
conda "r-nacho=2.0.5 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' }"

input:
path rcc_files
Expand Down
6 changes: 3 additions & 3 deletions modules/local/nacho/qc.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
process NACHO_QC {
label 'process_single'

conda "r-nacho=2.0.4 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
conda "r-nacho=2.0.5 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' :
'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' }"


input:
Expand Down