From 6f92a4d2e4d8649210a493d8b2140ec8cb045a90 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Thu, 10 Aug 2023 15:13:41 +0000 Subject: [PATCH 1/4] update mulled container --- modules/local/compute_gene_scores.nf | 6 +++--- modules/local/create_annotated_tables.nf | 6 +++--- modules/local/create_gene_heatmap.nf | 6 +++--- modules/local/nacho/normalize.nf | 6 +++--- modules/local/nacho/qc.nf | 6 +++--- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/local/compute_gene_scores.nf b/modules/local/compute_gene_scores.nf index e91684e..b06ed55 100644 --- a/modules/local/compute_gene_scores.nf +++ b/modules/local/compute_gene_scores.nf @@ -1,10 +1,10 @@ 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-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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-dfd42984f8ba1b1d0d13648f30430581dff51e82:2a27d1707e91426237b882a7ba5adec8724f9069-0' : - 'biocontainers/mulled-v2-dfd42984f8ba1b1d0d13648f30430581dff51e82:2a27d1707e91426237b882a7ba5adec8724f9069-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' : + 'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' }" input: path counts diff --git a/modules/local/create_annotated_tables.nf b/modules/local/create_annotated_tables.nf index aa417a2..5421348 100644 --- a/modules/local/create_annotated_tables.nf +++ b/modules/local/create_annotated_tables.nf @@ -1,10 +1,10 @@ process CREATE_ANNOTATED_TABLES { label 'process_single' - conda "r-nacho=2.0.4 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12" + conda "r-nacho=2.0.5 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12" container "${ 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 diff --git a/modules/local/create_gene_heatmap.nf b/modules/local/create_gene_heatmap.nf index df69cca..047e89d 100644 --- a/modules/local/create_gene_heatmap.nf +++ b/modules/local/create_gene_heatmap.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' : - 'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:e4b1ecb1e69304213c695190148317b26caa2841-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' : + 'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' }" input: path annotated_counts diff --git a/modules/local/nacho/normalize.nf b/modules/local/nacho/normalize.nf index 054ca64..26ccf5d 100644 --- a/modules/local/nacho/normalize.nf +++ b/modules/local/nacho/normalize.nf @@ -1,10 +1,10 @@ process NACHO_NORMALIZE { label 'process_single' - conda "r-nacho=2.0.4 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12" + conda "r-nacho=2.0.5 r-tidyverse=2.0.0 r-ggplot2=3.4.2 r-rlang=1.1.1 r-tidylog=1.0.2 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5 r-rcolorbrewer=1.1_3 r-pheatmap=1.0.12" container "${ 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 diff --git a/modules/local/nacho/qc.nf b/modules/local/nacho/qc.nf index 4186a4c..9e19c16 100644 --- a/modules/local/nacho/qc.nf +++ b/modules/local/nacho/qc.nf @@ -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: From 5de6f523fb3a1ec46436d538b0ed52521fe43b1b Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Thu, 10 Aug 2023 15:19:07 +0000 Subject: [PATCH 2/4] update CHANGELOG --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7509b90..f9bafb9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,9 +13,14 @@ 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) +- [#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) ### `Dependencies` +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| `nacho` | 2.0.4 | 2.0.5 | + ### `Deprecated` ## v1.1.1 - 2023-06-23 From 399cee0e54f038a990a23b920ca64c4985364956 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Fri, 11 Aug 2023 06:14:41 +0000 Subject: [PATCH 3/4] update container, conda string --- modules/local/compute_gene_scores.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/compute_gene_scores.nf b/modules/local/compute_gene_scores.nf index b06ed55..889a341 100644 --- a/modules/local/compute_gene_scores.nf +++ b/modules/local/compute_gene_scores.nf @@ -1,10 +1,10 @@ process COMPUTE_GENE_SCORES { label 'process_single' - 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" + 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 ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' : - 'biocontainers/mulled-v2-68b3ca19fcb1f8b052324cb635ab60f8b17a3058:27c800678a1e9e56c8b44f6a997464300938abdc-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-dfd42984f8ba1b1d0d13648f30430581dff51e82:2a27d1707e91426237b882a7ba5adec8724f9069-0' : + 'biocontainers/mulled-v2-dfd42984f8ba1b1d0d13648f30430581dff51e82:2a27d1707e91426237b882a7ba5adec8724f9069-0' }" input: path counts From 89a72cdaac2ecfab5147360e8ee794bfbf7c55d8 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Fri, 11 Aug 2023 06:16:00 +0000 Subject: [PATCH 4/4] update CHANGELOG --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f9bafb9..30c5f7e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,8 +12,9 @@ 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) -- [#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) +- [#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`